Process Description

JMP Genomics Browser

Many statistical hypothesis testing methods produce p-values. A p-value is the probability of observing that a test statistic is as or more extreme than the one computed from the data assuming that the relevant null hypothesis is true. The null hypothesis usually represents no association or relationship, and so, smaller p-values represent more evidence that the null is not true. The scale of evidence here is based on a type of probabilistic modus tollens, or argument by contradiction. A p-value is very often misinterpreted as the probability of the null hypothesis or as the probability of a false positive.

The JMP Genomics Browser can adjust columns of p-values for multiple testing as well as plot adjusted and transformed p-values using chromosomal positions. Results can be journaled by a group such as chromosome or candidate gene. The output data set also contains variables indicating significance and number of consecutive significant p-values according to the specified alpha level. Finally, a graphic representation of the gene can be overlaid onto the p-value plot to help you explore the significance and potential mechanism of differential expression.

What do I need?

One Input Data Set, containing the p-values of an arbitrary set of features (for example, genes, probesets, exons, or markers) is required for this process. The huex_1_mn_trimmed_bew_iqr_amr.sas7bdat data set serves as an example (containing a subset of Affymetrix human exon data, available in the JMP Genomics Sample Data\Copy Number folder), and is partially shown.

The input data set contains information about each probeset as well as expression values and other data for each gene. The -log10 p-values associated with each probeset are listed in the second to the last column (NLP_T3_Tissue_Type). Note that this is a tall data set; experimental conditions are listed in columns, whereas the individual genes are listed in rows.

The following files are optional:

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The Annotation Data Set. This data set contains information, such as gene identity or chromosomal location, for each of the markers or genes. This data set is a tall data set; each row corresponds to a different marker.

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The chromosome color theme settings file. This file is a SAS settings (.sas) file, generated from a text file using the Chromosome Color Theme process. This settings file defines the colors used to illustrate individual cytobands on a chromosome plot.

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The tracks settings file. This file is a SAS settings (.sas) file, generated from a text file using the Track Gene Text process. This settings file defines a track for a set of genes, and is used to embellish the p-value plot with depictions of genes.

For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.

Output/Results

Refer to the JMP Genomics Browser output documentation for detailed descriptions and guides to interpreting your results.