JMP Life Sciences Files are Identified by Suffixes

Typical analyses in JMP Life Sciences often generate a large number of output files and data sets. This is especially true when input and output files are contained with the same folder, when a process produces multiple output files, or when the same output folder is used for multiple processes. If any or all of these conditions occur, the number of files in a folder can multiply dramatically. How do you identify and distinguish between the different files? More importantly, how do you prevent overwriting existing files with the output of subsequent processes, particularly when all of the files tend to be similarly named?

JMP Life Sciences adds a unique suffix to each output file generated by a process. Suffixes are specific to each process and are dependent on the type of content contained in the file. These suffixes enable you to identify different output files and to correlate them with specific processes. All of the suffixes used by JMP Life Sciences are listed alphabetically in the table below. Each suffix is defined both by the process that generates it and by the contents of the file that carries it.

Note: Even with the suffixes, it is still possible to overwrite existing files. You should take care to specify different names for output files when doing multiple runs with the same input files. Alternatively, you can specify different output folders.

JMP Life Sciences Files have suffixes: Identification of output files by suffix, process, and contents.

File Suffix	Processes Generating the File	Function/Contents of the File
_aag	• Create Annotation Analysis Group Variables	Output data set listing the input data plus the annotation analysis group variable
_afr	• Marker Properties	Output data set containing allele frequencies
_afreqs	• Marker Properties	Output data set containing allele frequencies
_agc	• Correlation and Grouped Scatterplots	Output data set consisting of the input data merged with the annotation data set
_ags	• Correlation and Grouped Scatterplots	Output data set containing correlation statistics for each experimental group array pair
_alp	• Affymetrix Cytogenetics CHP Input Engine	Output data set
_amc	• ANOVA • Mixed Model Analysis	Output data set listing response and standardized residuals for each transcript cluster
_amr	• ANOVA	Output data set listing annotation information and various statistics for the most significant markers
_amr_sig	• ANOVA	Output data set containing the significant differences
_an0	• Recombination and Linkage Groups	Output data set listing the markers (and their positions) found on each chromosome
_anm	• ANOVA Normalization	Output data set with the same structure as the input data set but with normalized response variables
_anmbody	• ANOVA Normalization	Output HTML body content
_anmcontents	• ANOVA Normalization	Output HTML table of contents
_anmframe	• ANOVA Normalization	Output HTML incorporating the body and table of contents
_ann	• Copy Number/LOH Control Set Adjustment • Copy Number Partition	Output data set containing annotation information
_api	• Array Pseudo Image	Output data set listing the X- and Y-coordinates, probeset IDs, and intensities for each spot on the specified array
_ars	• ANOVA • One-Way ANOVA • Mixed Model Analysis	Output data set listing standardized residuals for each observations in the input data set
_as	• Relationship Matrix	Output data set listing the relationship matrix generated using the allele sharing similarity estimate
_asf	• Allele Specific Expression Filter	Output data set containing the filtering results
_asl	• Allele Specific Expression Filter	Output data set containing the design and ID variables, DNA and RNA matching variables, genotype group, and log ratio data of DNA and RNA
_asp	• Affected Sib-Pair Tests	Output data set containing affected sib-pair test statistics and .jsl file for plotting p-values
_asp_sbg	• Affected Sib-Pair Tests	Output data set listing the number of significant markers for the selected affected sib-pair tests
_asr	• Allele Specific Expression Filter	Output data set containing the log-ratio of RNA intensity data for estimated homozygous genotypes
_atan	• ArrayTrack	Annotation file created by ArrayTrack
_bin	• Copy Number Bin	Output data set listing the bins into which the probesets have been grouped. This data set also lists the physical position of the bin start site and the average intensity across the bin.
_binned	• Spectral 2D Bin	Output binned data
_bnm	• Batch Normalization	Output data set containing the batch-normalized data
_bnp	• Batch Normalization	Output data set containing the results of the principal components analysis
_bns	• Batch Normalization • Batch Scoring	Output data set containing mu and standard deviation across batches
_body	• SNP Power • Marker Properties • Haplotype Estimation • htSNP Selection • Feature Flagger	Output HTML body content
body	• Mixed Model Normalization	Output HTML body content
_Body	• Check Data Contents	Output HTML body content
_bowa	• Bivariate One-Way ANOVA	Output data set containing annotation data, and statistics on individual experiments and pair-wise comparisons
_box	• Distribution Analysis	Output data set listing the relative densities of spots on each array grouped by similar responses; used for drawing box plots
_bsb	• Batch Scoring	Output data set containing mu and standard deviation across batches
_bsc	• Batch Scoring	Output data set containing the batch-normalized data
_cca	• Case-Control Association	Output data set containing case-control association test statistics and .jsl file for plotting p-values
_ce	• Combine Experiments	Output data set generated from the merging of multiple tall SAS data sets
_ceb	• Column Enrichment	Output data set listing the categories that show results displaying significance as specified by the binary significance variables
_cec	• Column Enrichment	Output data set listing the categories that show results displaying significance as specified by the continuous significance variables
_ceexp	• Combine Experiments	Output experimental design data set
_cef	• Column Enrichment	Output data set containing the Fisher Exact test results for the binary significance variables
_cep	• Column Enrichment	Output data set containing PAGE results for the continuous variables.
_chrm	• Affymetrix Cytogenetics CHP Input Engine	Output data set
_cim_out	• QTL IM and CIM Analysis	Output data set listing position and associated LOD scores for each marker
_clm	• Compare Linkage Maps	Output data set containing map, linkage group, marker, distance, and other matching and ordering information
_cml	• QTL IM and CIM Analysis	Output data set listing the control markers used in the analysis
_cna	• Copy Number/LOH Control Set Adjustment	Output data set containing marker, location, and other annotation information
_cnae	• Copy Number/LOH Control Set Adjustment	Output data set containing experimental design information
_cnp_indata	• Copy Number Partition	Output data set containing input annotation data with additional output columns
_contents	• SNP Power • Marker Properties • Haplotype Estimation • htSNP Selection • Feature Flagger	Output HTML table of contents
contents	• Mixed Model Normalization	Output HTML table of contents
_Contents	• Check Data Contents	Output HTML table of contents
_cor	• Correlation and Principal Components • Cross Correlation	Output data set listing the correlation of all the different variables in the input data
_cov	• Correlation and Principal Components	Output data set listing the covariates of all the different variables in the input data
_cpg	• SNP-Trait Association • Imputed SNP Trait Association • Q-K Mixed Model • Marker-Trait Association • SNP-SNP Interactions	Output data set containing covariance parameter estimates for the genotype test. This data set is generated whenever any random effects are specified.
_cpt	• SNP-Trait Association • Imputed SNP Trait Association • Q-K Mixed Model • Marker-Trait Association • SNP-SNP Interactions	Output data set containing covariance parameter estimates for the trend test. This data set is generated whenever any random effects are specified.
_csn	• Control Set Normalization	Output data set containing the normalized data
_csne	• Control Set Normalization	Output experimental design data set
_dap	• Append	A concatenated data set resulting from appending the rows of two different data sets
_data	• Exon and Whole Transcript Expression CEL	SAS data set containing the imported data
_dc	• Difference Chooser	Output data set containing LSMeans differences. Useful in ANOVA-related processes.
_den	• Distribution Analysis	Output data set used for plotting the overlaid kernel density estimate plot
_det	• Spectral 2D Peak Find	Output data set containing detailed information for each peak
_dge	• Distribution Analysis	Output experimental design data set when using Group variables
_dgm	• Distribution Analysis	Output data set when using Group variables
_dlb	• Change Labels	Output data set in which the variables of the original data set have been relabeled
_dln	• Change Lengths	The output data set in which the lengths of the variables of the original data set have been resized
_dmg	• Merge	The large data set resulting from merging two smaller data sets
_dmt	• Distance Matrix	Output data set listing the measures of dissimilarity between all pairs of observations in the experiment
_drk	• Rank Rows	The output data set in which the individual values within each variable have been replaced with the ranking of that observation within the variable
_drn	• Rename	The output data set in which the primary variables of the original data set have been renamed
_dro	• Reorder	The output data set in which the order of the variables in the original data set has been changed
_drs	• Statistics for Rows	Data set listing row-wise statistics for the primary data set. Rows meeting the criteria specified in the Delete Rows Satisfying this Expression box on the Options tab are excluded from the data set.
_dsa	• Discriminant Analysis	Output data set containing all of the data from the input data set plus three additional columns. These include observation number, and two columns listing the predicted values for the dependent class variable.
_dsav	• Discriminant Analysis	Lists the names of the variables selected and used for making predictions
_dsm	• Statistics for Columns	Data set listing summary statistics for the variables in the primary data set
_dso	• Distance Scoring	Lists the statistics and associated predictions for each of the individuals in the input data set
_dsov	• Distance Scoring	Lists the names of the variables selected and used for making predictions
_dsp	• Data Step	The modified data set resulting from executing SAS data step commands on a data set
_dss	• Subset	Output subset data set
_dst	• Sort Rows	The output data set in which the variables in the input data set have been sorted according to specified key variables
_dt	• Spectral 2D Detrend	Output detrended data set
_dtf	• Transform	The output data set resulting from the mathematical transformation of specified variables in a primary data set
_dtr	• Transform Rectangular	The data set resulting from the transposition of a block of variables in the original data set
_eg	• Expand Multiallelic Genotypes	Output data set with multiallelic genotypes expanded into one column per allele
_eg_anno	• Expand Multiallelic Genotypes	Output annotation data set associating expanded genotype markers with markers
_eig	• Correlation and Principal Components • Relationship Matrix	Output data set listing the Eigenvalues and associated experimental statistics
_eigenval	• PCA for Population Stratification	Output data set containing eigenvalues and cumulative variance for PCs
_esc	• Gene Set Scoring	Output data set containing the scored data
_est	• Estimate Builder/Compare Means	Output file containing the estimate statements
_exp	• Many different input engines, data set utilities and analytical processes	Experimental Design Data Set (EDDS)
_ffi	• Feature Flagger	Output data set in which individual values for the variables have been replaced with "0", if values are within defined parameters, or "1", if values are outside of those parameters
_fin	• Filter Intensities	Output data set listing the filtered intensities
_fnm	• Factor Analysis Normalization	Output data set with the same structure as the input data set, but with normalized response variables
_fp	• Meta-Analysis • GWAS Meta-Analysis (Forest Plot action button)	Output data set containing statistics for forest plot
_frame	• SNP Power • Marker Properties • Haplotype Estimation • htSNP Selection • Feature Flagger	Output HTML incorporating the body and table of contents
frame	• Mixed Model Normalization	Output HTML incorporating the body and table of contents
_Frame	• Check Data Contents	Output HTML incorporating the body and table of contents
_fs	• Flip Strand	Output annotation data set containing corrected strandedness for major/minor alleles
_gea	• GxE Interaction	Output data set containing ANOVA statistics
_gee	• GxE Interaction	Output data set containing stability statistics
_gel	• GxE Interaction	Output data set containing genotype LS means
_gem	• GxE Interaction	Output data set containing GxE LS means
_gen	• GxE Interaction	Output data set containing ANOVA from linear-bilinear model
_gep	• GxE Interaction	Output data set containing PCA statistics
_ges	• GxE Interaction	Output data set containing scree plot statistics for PCs
_gfr	• Marker Properties	Output data set containing genotype frequencies
_gfreqs	• Marker Properties	Output data set containing genotype frequencies
_glm	• General Linear Model Selection	Lists the statistics and associated predictions for each of the individuals in the input data set
_glmv	• General Linear Model Selection	Lists the names of the variables selected and used for making predictions
_gma	• GWAS Meta-Analysis • Meta Analysis	Output data set containing meta-analysis p-values and heterogeneity statistics
_gma_sbg	• GWAS Meta-Analysis	Output data set listing the number of significant markers for the selected association tests
_gms	• Gene Model Summary	Output data set containing the summarized data
_gp	• Build Genotype Probability Data Set	Output data set listing the probabilities of observing specific QTL genotypes at each one cM interval along the chromosome(s)
_gse	• Gene Set Enrichment	Output data set containing enrichment test results
_gsei	• Gene Set Enrichment	Output data set containing 0-1 indicator variables for the categories
_gtt	• Hy’s Law Screening	Graph Time Trends drill down data set.
_hc	• Hierarchical Clustering	Output data set containing all of the variables from the input data set plus results (row means and standard values, the cluster to which each belongs and its place within the cluster) of the hierarchical clustering
_hest	• Haplotype Estimation	.html output files, .jsl file for plotting p-values, and output data set containing association test statistics
_hfr	• Haplotype Estimation	Output data set containing haplotype frequency estimates that can be used as input to the htSNP Selection process
_her	• Haseman-Elston Regression	Output data set containing Haseman-Elston regression test statistics and .jsl file for plotting p-values
_her_sbg	• Haseman-Elston Regression	Output data set listing the number of significant markers for the tests
_hph	• Haplotype Estimation	Output data set containing phase assignment probabilities. This data set can be used as the input data set for the Haplotype Trend Regression process.
_hrg	• Haplotype Trend Regression	Output data set containing dependent variable(s), window, and F-statistic information.
_hrs	• Haplotype Trend Regression	Output data set containing dependent variables, haplotype and name, window, and F-statistic information.
_hti	• htSNP Selection	Output data set that contains all the columns from the annotation data set with an additional htSNP Indicator column
_htr	• Haplotype Trend Regression	.html output files
_hts	• htSNP Selection	.html output files, .jsl file for displaying htSNPs, and output data set containing htSNP information
_hwe	• Marker Properties	Output data set containing HWE test statistics and other marker properties
_hwe_sbg	• Marker Properties	Output data set listing the number of significant markers for the HWE test
_hwetest	• Marker Properties	Output data set containing HWE test statistics and other marker properties
_ibd	• Relationship Matrix	Output data set listing the relationship matrix generated using the identical by descent estimate
_ibs	• Relationship Matrix	Output data set listing the relationship matrix generated using the identical by state estimate
_igp	• Imputed SNP (Wide Format) • Imputed SNP (Tall Format)	Stacked output genotype probabilities SAS data set containing probabilities for each genotype at a SNP
_igt	• Imputed SNP (Wide Format) • Imputed SNP (Tall Format)	Output genotype threshold SAS data set listing the most likely genotype for each SNP
_ipm	• Marker Properties	Output data set containing the proportion of missing genotypes
_iqr	• Data Standardize	Output data set containing the IQR standardized values for the input data set
_isr_N	• IBS Sharing Regions	Output data set for chromosome N in tall format with sample genotypes, IBS sharing count, and run statistics
_iss	• IBS Sharing Regions	Output data set with lengths and spans of runs across all chromosomes
_ist	• Imputed SNP-Trait Association	Output data set containing association test statistics and .jsl file for plotting p-values
_ist_sbg	• Imputed SNP-Trait Association	Output data set listing the number of significant markers for the selected association tests
_itt	• IBS Sharing Regions	Output data set
_jnm	•	Output data set containing SU normalized data
_jnp	•	Output data set listing the four estimated parameters for each array used to generate the SU normalized data
_kc	• K Matrix Compression	Output data set containing the compressed matrix
_kcf	• K Matrix Compression	Output data set containing the criteria for optimal compression level, the corresponding values, and number of clusters generated during the compression
_kcv	• K Matrix Compression	Output data set containing the covariance parameter estimates from every model fit during the compression
_kmc	• K-Means Clustering	Lists the center of each cluster and the corresponding statistics
_kmd	• K-Means Clustering	Lists the statistics for each observation, the cluster to which the observation has been assigned, and its distance from the cluster mean
_kmf	• KDMM Normalization	Output data set containing KDMM scaling factor and total mapped reads for each sample
_kml	• KDMM Normalization	Output data set containing log-transformed KDMM normalized data
_kmm	• KDMM Normalization	Output data set containing KDMM normalized data
_kmp	• KDMM Normalization	Output data set containing A and M component, and kernel density, for each sample
_kmx	• Kinship Matrix	Output data set consisting of the input data modified to identify the parents of the different pedigrees and matrix statistics
_knn	• K-Nearest Neighbors	Lists the statistics and associated predictions for each of the individuals in the input data set
_knnv	• K-Nearest Neighbors	Lists the names of the variables selected and used for making predictions
_ld	• Linkage Disequilibrium	.jsl file for displaying LD results
_ldbb	• LD Block Creation	Output data set listing detailed LD block information (first and last marker and location, and block size and length) for every block in every chromosome
_ldbc	• LD Block Creation	Output data set listing the name, location, LD block, and annotation information for each of the SNPs
_ldbs	• LD Block Creation	Output data set listing Dprime, locus, distance, AbsDprime, and other information for every pair of markers
_ldbs_N	• LD Block Creation	Output data set listing Dprime, locus, distance, AbsDprime, and other information for every pair of markers within annotation group variable N (for example, chromosome)
_ldc	• Linkage Disequilibrium	Output data set containing LD measures used in the Contour Plot and/or the LD Decay plot
_ldc_N	• Linkage Disequilibrium	Output data set containing LD measures used in the Contour Plot and/or the LD Decay plot, within annotation group variable N
_ldm	• Linkage Disequilibrium	Output data set containing haplotype, frequency, D, correlation coefficient, Dprime, delta, and other statistics for each pair of markers
_lds	• Linkage Disequilibrium	Output data set containing LD test statistics
_lds_N	• Linkage Disequilibrium	Output data set containing LD test statistics within annotation group variable N
_ldts	• LD tagSNP Selection	Output data set containing tagSNP information
_ldts_body	• LD tagSNP Selection	.html output file summarizing the tagSNP information
_len	• List Enrichment	Output data set containing the list enrichment statistics
_lgr	• Logistic Regression • SNP Interaction Discovery • Recombination and Linkage Groups	Output data set containing all of the data from the input data set plus three additional columns. These include observation number, and two columns listing the predicted values for the dependent class variable.
_lgrv	• Logistic Regression • SNP Interaction Discovery	Lists the names of the variables selected and used for making predictions
_lite	• Copy Number Partition	Output data set containing physical position, sample, chromosome, segment start and end, intensity information, and other statistics
_lkmp	• Linkage Map Viewer	Output data set containing marker name, linkage group, original and map order, distance, and other information
_lmo	• Linkage Map Order	Output data set containing marker name, linkage group, original and map order, distances, and other order statistics
_lmr	• Linkage Map Order	Output data set containing marker pairs, recombination rate, linkage group, locus, and other information
_lnm	• LoessNormalization	Output data set containing the loess normalized data
_lnp	• Loess Normalization	Output data set containing data used for drawing the M-A plots
_lsm	• SNP-SNP Trait Association • Pleiotropic Association • Q-K Mixed Model • SNP-SNP Interactions	Output data set containing genotype LS means and differences
_map	• Imputed SNP (Tall Format) Input Engine	Output data set containing annotation marker map information
_mcp	• Multiple SNP-Trait Association	Output data set containing multiple-locus regression covariance estimates
_mcpp	• Multiple SNP-Trait Association	Output data set containing PCA regression covariance estimates
_mdf	• Multidimensional Scaling	Output data set listing statics from the multidimensional scaling process
_mdr	• Multidimensional Scaling	Output data set listing the statistics for and distances between pairs of observations from the input data set
_mds	• Multidimensional Scaling	Output data set listing the multi-dimensional coordinates of each observation
_mea	• Data Standardize	Output data set containing the mean standardized values for the input data set
_med	• Data Standardize	Output data set containing median standardized values
_meds	• Data Standardize	Output data set containing location and scale estimates used to median-center the input values
_metadata	• Copy Number Partition	Output metadata table.
_mgs	• Missing Genotype by Trait Summary	Output data set listing the counts of genotyped cases and controls, the number of missing genotypes for cases and controls, and the statistics for testing for different missing proportions between cases and controls for each marker
_mgs_sbg	• Missing Genotype by Trait Summary	Output data set listing the number of significant markers for missing test, for each value of the annotation group variable
_mld	• Malecot LD Map	.jsl file for creating plots and output data set containing estimates of LDU between pairs of markers
_mml	• Malecot LD Map	Output data set containing estimates for parameters M and L
_mmp	• Mixed Model Power	Output data set listing power values and associated t-statistics for a set of hypothesis tests for a range of alpha and effects sizes
_mmr	• Mixed Model Analysis	Lists annotation and statistical information for each of the groups
_mmr_sig	• Mixed Model Analysis	Output data set containing the significant differences
_mnm	• Mixed Model Normalization	Output data set with the same structure as the input data set but with both the original and the normalized response variables
_mpe	• Multiple SNP-Trait Association	Output data set containing multiple-locus regression parameter estimates
_mpep	• Multiple SNP-Trait Association	Output data set containing PCA regression parameter estimates
_mrs	• Mixed Model Analysis	Output residual data set
_msd	• Merge Gene Sets	Output merged data set
_mst	• Multiple SNP-Trait Association	Output data set containing association test statistics
_mtr	• Merge and Transform	The output data set resulting from the merging of two sets sharing a common set of variables and the subsequent computation of an arbitrary function for each pair of variables sharing the same name
_mta	• Marker-Trait Association	Output data set containing association test statistics and .jsl file for plotting p-values
_mta_sbg	• Marker-Trait Association	Output data set listing the number of significant markers for the selected association tests
_mvi	• Missing Value Imputation	The complete output data set in which values missing from the input data set have been imputed from the non-missing values in the same row
_names	• Nexus	Output data set containing names of markers
_num	• Marker Properties	Output data set containing numerically coded genotypes used in subsequent processes
_numgeno	• Marker Properties	Output data set containing numerically coded genotypes used for the cell plot
_numgeno (by default, or other Prefix for Column Names specified)	• Recode Genotypes	Output data set with recoded genotypes
_one	• Single Marker Analysis	Output data set listing the results of the regression analysis and -log2 p-values for association of each of the markers with each of the two quantitative traits, along with annotation information for each of the markers
_org	• Q-K Mixed Model • SNP-SNP Interactions • SNP-Trait Association	Output data set containing residuals from genotype test
_ort	• PCA for Population Stratification • Q-K Mixed Model • SNP-SNP Interactions • SNP-Trait Association	Output data set containing residuals from trend test
_owa	• One-Way ANOVA	Output data set containing annotation data, and statistics on individual experiments and pair-wise comparisons
_owa_sig	• One-Way ANOVA	Output data set containing the significant differences
_pca	• Principal Components Analysis for Population Stratification • Principal Components Analysis	Output data set listing the row scores for each of the principal components
_pce	• PCA for Population Stratification	Output data set containing EigenCorr statistics for PCs
_pcm	• Principal Components Analysis for Population Stratification	Output data set containing the PCA data merged into the input data set
_peg	• SNP-Trait Association • Survey SNP-Trait Association • Pleiotropic Association • Marker-Trait Association • SNP-SNP Interactions	Output data set containing the parameter estimates for the genotype test
_pet	• SNP-Trait Association • Survey SNP-Trait Association • Imputed SNP-Trait Association • PCA for Population Stratification • Pleiotropic Association • Marker-Trait Association • SNP-SNP Interactions • QTL Single Marker Analysis	Output data set containing the parameter estimates for the trend test
_pi	• Plot Intensities	Output data set containing raw intensities and row statistics for the input data set
_pla	• Pleiotropic Association	Output data set containing association test statistics for MANOVA and individual trait tests
_pla_sbg	• Pleiotropic Association	Output data set listing the number of significant markers for the selected association tests
_plr	• SNP Interaction Discovery	Output data set containing all of the data from the input data set plus three additional columns. These include observation number, and two columns listing the predicted values for the dependent class variable.
_plrv	• SNP Interaction Discovery	Lists the names of the variables selected and used for making predictions
_pls	• Partial Least Squares	Lists the statistics and associated predictions for each of the individuals in the input data set
_plsv	• Partial Least Squares	Lists the statistics associated with the ability of each marker to be used as a predictor for the dependent class variable
_pmd	• Population Measures	Output symmetric matrix of dissimilarities between specified groups within a study
_pmf	• Population Measures	Output data set listing the individual F-statistics for each marker
_pmg	• Pleiotropic Association	Output data set containing MANOVA test statistics for genotype test
_pmo	• Population Measures	Output data set listing the overall F-statistics for the population
_pmt	• Pleiotropic Association	Output data set containing MANOVA test statistics for trend test
_pps	• Principal Components Analysis for Population Stratification	Output data set listing each of the markers with selected annotation data and the resulting probabilities the markers are associated with the disease trait, given population stratification
_pnm	• Effect Removal via PLS Normalization • Partial Least Squares Normalization	Output data set with the same structure as the input data set but with normalized response variables
_prs	• Relationship Matrix	Output data set listing pairs of samples having an identical-by-descent value exceeding a specified threshold
_psc	• Phenotype Summary	Output data set containing counts for categorical variables
_psq	• Phenotype Summary	Output data set containing counts for quantitative variables
_ptr	• Partition Trees	Output data set listing the input data that has been recursively partitioned to optimal splitting relationships as determined by the specified dependent and predictor variables
_ptrv	• Partition Trees	Lists the names of the variables selected and used for making predictions
_pva	• P-Value Adjustment	Output data set containing the columns in the input data set with four additional columns listing the adjusted p-values for each set of observations
_pvb	• P-Value Browser	Output data set containing the columns in the input data set with four additional columns listing the adjusted p-values for each set of observations
_pvc	• Correlation and Principal Components	Output data set containing the variance within each of the principal components that can be attributed to each of the variance components
_pvc	• P-Value Combination	Output data set containing combined p-values
_qcbp	• Exon and Whole Transcript Expression CEL	Output data set that is used to create a pseudoimage of the arrays
_qkm	• Q-K Mixed Model	Output data set containing association test statistics and .jsl file for plotting p-values
_qnm	• Quantile Normalization	Output data set containing the quantile normalized data
_qnp	• Quantile Normalization	Output data set containing the quantile normalized data along with relative rank of each observation and residual data
_qtdt	• Quantitative TDT	Output data set containing Q-TDT test statistics and .jsl file for plotting p-values
_qtdt_sbg	• Quantitative TDT	Output data set listing the number of significant markers for the selected association tests
_rai	• Ratio Analysis	Output data set containing the log intensities of the input data
_rar	• Ratio Analysis	Output data set containing the log ratio of the two-channel input data
_ratio	• Ratio Analysis	Output data set containing a condensed version of the input experimental design data set, reorganized in terms of the variable defining the ratio
_rbm	• Radial Basis Machine	Lists the statistics and associated predictions for each of the individuals in the input data set
_rbmv	• Radial Basis Machine	Lists the names of the variables selected and used for making predictions
_rm	• Relationship Matrix	Data set containing the root matrix as computed by single value decomposition (SVD) appended to the input data set
_rmg	• Recode Missing Genotypes	Output data with missing genotypes recoded to SAS missing values
_rpf	• RPM Scaling	Output data set containing RPM scaling factor and total mapped reads for each sample
_rpl	• RPM Scaling	Output data set containing log-transformed RPM normalized data
_rpm	• RPM Scaling	Output data set containing RPM normalized data
_rules	• Copy Number Partition	Output data set containing overall worth and rules data
_rva	• Rare Variant Association	Output data set containing rare variant association test statistics
_s2b	• 2D Bin	Output data set containing the binned values for each variable
_s2d	• 2D Detrend	Output data set containing the baseline-adjusted and corrected values
_s2p	• 2D Peakfind	Output data set identifying each peak found in each trace
_s2p_det	• 2D Peakfind	Output data set providing specific information (upper and lower boundaries, height, area, for example) for each peak identified in each trace
_s2g	• 2D Plot	Output data set listing trimmed input values
_s3a	• 3D Align	Output data set listing the X and Y coordinates for each row with the Z values for each sample listed in a separate column
_s3g	• 3D Plot	Output data set listing the X and Y coordinates for each row with the Z values for each sample listed in a separate column
_sbg	• Case-Control Association • PCA for Population Stratification • Marker-Trait Association • SNP-Trait Association • Imputed SNP-Trait Association • Survey SNP-Trait Association • Q-K Mixed Model • Quantitative TDT • TDT • GWAS Meta-Analysis • Multiple SNP-Trait Association • Rare Variant Association • Pleiotropic Association	Output data set listing the number of significant markers for the selected association tests
__sbg	• Q-K Mixed Model	Output data set listing the number of significant markers for the selected association tests
_sdp	• Affymetrix Cytogenetics CHP Input Engine	Output data set
_seq	• Affymetrix Tiling CEL Input Engine	Output sequence data set
_sfg	• SNP-Trait Association	Output data set containing survival function estimates for genotype test
_sfs	• Surface Summary	Output data set containing the estimated surface
_sft	• SNP-Trait Association	Output data set containing survival function estimates for trend test
_sgc	• Affymetrix Cytogenetics CHP Input Engine	Output data set
_sgl	• Affymetrix Cytogenetics CHP Input Engine	Output data set
_sma	• QTL Single Marker Analysis	Output data set containing chromosome number and label, marker position and label, trait, effect, and several estimates and test statistics
_sma_sbg	• QTL Single Marker Analysis	Output data set listing the number of significant markers for the trend test
_smc	• Affymetrix Cytogenetics CHP Input Engine	Output data set
_snl	• Affymetrix Cytogenetics CHP Input Engine	Output data set
_sp	• Exon and Whole Transcript Expression CEL	Output data set that lists single-probes not associated to any probeset
_spmm	• Survival Predictive Modeling	Output data set listing mean survival times
_spms	• Survival Predictive Modeling	Output data set listing survival functions corresponding to the training data set
_spmt	• Survival Predictive Modeling	Output data set listing survival functions corresponding to the test data set
_spmv	• Survival Predictive Modeling	Output data set listing the effects applied in the Cox model
_sps	• Exon and Whole Transcript Expression CEL	Output data set that lists single-probe-sets not associated to any transcript cluster
_sr	• Subset and Reorder Genetic Data	The output data set resulting from the reordering/removal of markers or individuals from either a genotype or annotation data set
_sr_d	• Subset and Reorder Genetic Data	The output annotation data set containing excluded markers only
_ssi	• SNP-SNP Interactions	Output data set containing SNP-SNP association test p-values
_sst	• Survey SNP-Trait Association	Output data set association test statistics
_sst_sbg	• Survey SNP-Trait Association	Output data set listing the number of significant markers for the selected association tests
_sta	• SNP-Trait Association • PCA for Population Stratification	Output data set containing association test statistics and .jsl file for plotting p-values
_sta_sbg	• SNP-Trait Association	Output data set listing the number of significant markers for the selected association tests
_stacked	• Copy Number Partition	Output data set containing sample, chromosome, physical position, intensity, segment start and end, and other information
_std	• Data Standardize	Output data set with the same structure as the input data set but response variable values that have been standardized using one or more different methods
_stk	• Stack	Output stacked data set
_sub	• Check Data Contents	Output subset data set
_sumrules	• Copy Number Partition	Output data set containing sample, chromosome, and position columns
_sumstats	• Copy Number Partition	Output data set containing rules, intensity, and positioning columns
_sva	• Survival Analysis	Output data set listing survival statistics
_svd	• Calculate Square Root of Matrix	Output data set
_tal	• Transpose Tall and Wide • Unstack	The tall data set resulting from either the transposition of a wide data set or the unstacking of a stacked data set. Note: These processes also generate an associated EDDS.
_tdt	• TDT	Output data set containing TDT statistics and .jsl file for plotting p-values
_tdt_sbg	• TDT	Output data set listing the number of significant markers for the selected association tests
_tdtt	• TDT	Output data set containing a pair of allelic transmission scores for each individual at each marker locus
_tmf	• TMM Normalization	Output data set containing TMM scaling factor and total mapped reads for each sample
_tml	• TMM Normalization	Output data set containing log-transformed TMM normalized data
_tmm	• TMM Normalization	Output data set containing TMM normalized data
_tmp	• TMM Normalization	Output data set containing MA plot data
_tst	• Correlation and Principal Components • Cross Correlation	Output data test data set containing the p-values for the test that the correlation equals zero
_uqf	• Upper Quartile Scaling	Output data set containing upper quartile scaling factor and total mapped reads for each sample
_uql	• Upper Quartile Scaling	Output data set containing log-transformed upper quartile normalized data
_uqs	• Upper Quartile Scaling	Output data set containing upper quartile normalized data
_vc	• Correlation and Principal Components • Batch Normalization	Output data set containing variance component estimates computed from the principal components
_vcp	• Variance Components	Output data set listing each of the markers with selected statistics for the chi-square statistics and p-values for the likelihood ratio test or the z-scores and p-values for the Wald test that test for linkage between each marker and the quantitative trait
_vcp_sbg	• Variance Components	Output data set listing the number of significant markers for the selected test
_vg	• Verify Gender of Samples	Output data set listing the genetic sex of the individuals
_vgs	• Verify Gender of Samples	Output data set listing the genetic sex of the individuals, without the marker variables
_wid	• Transpose Tall and Wide	The wide data set resulting from the transposition of a tall data set
_z	• Surface Summary	Output coordinates data set