Process Description

Affymetrix Copy Number CHP Input Engine

The Affymetrix CN CHP Input Engine imports multiple CNCHP and/or LOHCHP files into a single SAS data set with rows representing probeset identifiers and columns containing various copy number and/or loss of heterozygosity measurements for each of the samples.

What do I need?

Before you can successfully import the raw data into SAS data sets that can be used for analysis in JMP Genomics, you must locate and gather different sources of information:

•

The folder containing the .cnchp files obtained by processing SNP .cel files using the Affymetrix Genotyping Console. These .cnchp files, each corresponding to an individual microarray, contain summarized copy number information and specific information about the format of the chip.

•

The Experimental Design File (EDF) for the experiment. The EDF lists specific information about the design of the experiment. The EDF is typically a text file or Excel spread sheet and must be created before the data can be imported. The edf_cn5_2obs.sas7bdat EDF used in the following example, was generated using the Create a Design Data Set from an Existing Data Set process. This EDF was placed in a new Copy Number folder that was created in the Sample Data folder that comes with JMP Genomics.

The following example uses CNCHP files created from .cel files in Affymetrix Genotyping Console, from an X titration data set available for download from Affymetrix. Two compressed files, NA01416_5X.rep1.CN5.cnchp and NA01416_5X.rep2.CN5.cnchp, containing LOH and CN data, were downloaded from the Affymetrix website, unzipped, and saved to a folder named Copy Number, located in the Sample Data folder that comes with JMP Genomics.

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

Output/Results

The output data sets generated by this process are listed in a Results window. Refer to the Affymetrix Copy Number CHP Input Engine output documentation for detailed descriptions.