Process Description

Affymetrix Tiling CEL Input Engine

Unlike normal microarrays, which typically include a limited number of spaced, non-overlapping, probes for each known gene, tiling arrays contain many overlapping probes designed to cover large contigs of the genome, or even the whole genome itself. Because of their potential for very high resolution, and coverage, tiling arrays can produce a much more unbiased examination of overall expression of both known and unidentified genes. However, because of the extreme number of probes, the .cel files containing the data tend to be very large.

The Affymetrix Tiling CEL Input Engine enables you to import data and other information contained in Affymetrix .cel files into these SAS data sets.

Note: This input engine does not function in client/server mode.

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 three different sources of information:

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The folder containing the raw data files. These .cel files, each corresponding to an individual microarray, contain the hybridization intensities.

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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. Note: The EDF used for importing tiling data must contain a variable called SampleName. The values listed in this column identify each sample in the experiment. Providing this name allows the tiling data for each sample, which are typically spread across multiple .cel files, to be merged into one SAS data set.

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One or more specific binary probe map (.bpmap) library files. These files, which are available for download from Affymetrix, using the NetAffx Download Engine process, contain information used to associate individual data points extracted from the .cel files with corresponding probesets.

The following example uses the NCBI GEO GSE15220 data set. These data, from a study of testicular cancer, are spread across 42 different .cel files. Due the size of the files, this example includes only four .cel files. This data set was downloaded from the Affymetrix website and placed in a new Affymetrix Tiling folder created in the Genomics\Sample Data folder.

The ExpDesign.txt file has been selected as the EDF. Note the required SampleName column.

The Hs35b_P01R_v01-3_NCBIv34.bpmap file, which was downloaded from the Affymetrix website and placed in a new Affymetrix Tiling folder, serves as the BPMAP file for this example.

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 Tiling CEL Input Engine output documentation for detailed descriptions.