Output Description

Affymetrix Cytogenetics/CytoscanHD CHP Input Engine

The output generated by this process are listed in a Results window. Refer to Affymetrix Cytogenetics/CytoscanHD CHP Input Engine for a description of the output data and files generated by this process.

The Results window contains the following elements:

Output Data

The number of output SAS data sets generated depends on the array type and input data provided. Note:The example described in the Affymetrix Cytogenetics/CytoscanHD CHP Input Engine process description results in the generation of the following eleven SAS data sets:

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Output Experimental Design Data Set: This data set lists specific information about experimental details for each of the arrays. This data set is generated when the input data is derived from either the 2.7M Cytogenetic arrays or the CytoScanHD arrays. Refer to Experimental Design Data Set (EDDS) for general information about this data set.

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Intensity Data Set: (Also know as the Copy Number Data Set or the Output Data Set). This data set contains the data from the different .chp files and is generated when the input data is derived from either the 2.7M Cytogenetic arrays or the CytoScanHD arrays. This data set is typically very large; so large, in fact, that opening it can severely tax the memory of most desktop computers and servers. Clicking View Subset opens and runs the Check Data Contents process for the output data. This is a useful and quick method for viewing a subset of an extremely large data set, allowing you to verify that the data were imported correctly.

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CHP Header Data Set: This data set contains all the parameters in the header portion of each .cychp file and is generated when the input data is derived from either the 2.7M Cytogenetic arrays or the CytoScanHD arrays. These parameters include the algorithm applied, the type of chip used, the program applied, and other quality control information among the control l probes. The parameters are listed in columns, while the individual .cychp files are listed in rows.

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Annotation Data Set: This data set is a modified version of the input annotation data set and is generated when the input data is derived from either the 2.7M Cytogenetic arrays or the CytoScanHD arrays. The order of the rows has been sorted to match the order of the SN markers in the output data set.

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Allele Peaks Data Set: This data set lists a summary of the allele patterns and is generated when the input data is derived from either the 2.7M Cytogenetic arrays or the CytoScanHD arrays.

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Chromosome Summary Data Set: This data set lists summary information for each chromosome. It is generated when the input data is derived from either the 2.7M Cytogenetic arrays or the CytoScanHD arrays.

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Segments CN Data Set: This data set lists segment data for copy number analysis. It is generated when the input data is derived from either the 2.7M Cytogenetic arrays or the CytoScanHD arrays.

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Segments LOH Data Set: This data set lists segment data for determining LOH status. It is generated when the input data is derived from either the 2.7M Cytogenetic arrays or the CytoScanHD arrays.

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Segments CNNeutralLOH Data Set: This data set lists CN and LOH states for the segments. It is generated when the input data is derived from either the 2.7M Cytogenetic arrays or the CytoScanHD arrays.

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Segments NormalDiploid Data Set: This data set defines segments showing normal diploid status. It is generated only when the input data is derived from the 2.7M Cytogenetic arrays.

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Segments Mosaicism Data Set: This data set summarizes segment CN state and mosaicism. It is generated only when the input data is derived from the 2.7M Cytogenetic arrays.

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Genotyping Calls Data Set: This data set list genotype calls. It is generated only when the input data is derived from the CytoScanHD arrays (It was not generated for this example.).

Note: You can view the data in a file or data set by clicking either Open or View Subset (when the data set is very large).

Note: You should download the Affymetrix GCOS 1.x and Command Console (project “Calvin) file formats documentation and refer to the cychp.html file for detailed information about these data sets and their contents.

Launch Follow-up Processes

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Basic Copy Number Workflow: Click Basic Copy Number Workflow to launch the Basic Copy Number Workflow process with the output data set, EDDS, and annotation data set specified as input.

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Copy Number Partition: Click Copy Number Partition to launch the Partition process with the output data set and the annotation data set specified as input.

General

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Click Reopen Dialog to reopen the completed process dialog used to generate this output.

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Click Close All to close all graphics windows and underlying data sets associated with the output.