Process Description

Affymetrix Cytogenetics/CytoscanHD CHP Input Engine

The Affymetrix Cytogenetics/CytoscanHD CHP Input Engine enables you to import data, experimental design variables, and other information contained in Affymetrix .cychp (signal data) files into SAS data sets. See the Output/Results section for a table summarizing these SAS data sets.

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:

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The folder containing the raw data files. These .cychp files, each corresponding to an individual microarray, contain the hybridization intensities and specific information about the format of the chip.

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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.

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One or more specific library files, available for download from Affymetrix, that contain information used to associate individual data points extracted from the .cychp files with corresponding probesets, might be required for importing .cychp files that were formatted before the introduction of the AGCC format used by the Affymetrix Expression Console.

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An Annotation Data Set. This data set provides annotation information, such as gene names, function, physical location, and association, for each of the markers used in the analysis. This data set must have a variable named Probe_Set_ID that is used to correctly order the SNPs in the output data set.

Tip: The appropriate annotation file can be downloaded from the Affymetrix website using the NetAffx Download Engine process found under the Genomics > Import > Affymetrix menu. Once you have downloaded the appropriate annotation .csv file, select Genomics > Import > Affymetrix > Annotation CSV to import this file into a SAS data set.

The following example uses a subset of the ChAS sample data series provided by Affymetrix. The compressed files were downloaded from the Affymetrix website, unzipped, and saved to a new folder named Affy Cytogenetics CHP IE, created in the Sample Data folder that is included with JMP Genomics. Included .cychp files are listed below.

Additional files include the Cytogenetics_Array.cdf CDF and the _cytogenetics_array_na29_annot.sas7bdat annotation file.

The first step in importing the data contained in the .cychp files was to generate an Experimental Design File (EDF) using the Create Design File Template process. The resulting EDF.jmp file was opened in JMP and the required ColumnName column was generated using the Create ColumnName process. The values in this column were generated by concatenating the values in the Array and File columns. Finally, the modified EDF file was renamed and saved in the Affy Cytogenetics CHP IE folder as the edf_cychp_2_7m2.sas7bdat file.

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 Cytogenetics/CytoscanHD CHP Input Engine output documentation for detailed descriptions.