Note: If you are using Excel to edit GenePattern files, be sure to save the file as a tab-delimited text file and supply the correct file extension. You can specify the file name in quotes to prevent Excel from appending .txt to the file name. Also, note that Excel's auto-formatting can introduce errors in gene names, as described in Zeeberg, et al (2004).
XCN File Format
This is a tab-delimited file format that is similar to the SNP file format, but contains SNP copy numbers rather than SNP intensity values. It contains one row for each SNP and two columns for each SNP array: the raw copy number value and the call value. It is organized as follows:
The first line contains a list of labels identifying the SNP arrays.
SNP (tab) Chromosome (tab) PhysicalPosition (tab) (array_1_name) (tab) (array_1_name) Call (tab) ... (array_N_name) (tab) (array_N_name) Call
SNP (tab) Chromosome (tab) PhysicalPosition (tab) MYNAH_p_Affy_plate_9_Mapping250K_Sty_A01_49068 (tab) MYNAH_p_Affy_plate_9_Mapping250K_Sty_A01_49068 Call (tab) ... MYNAH_p_Affy_plate_9_Mapping250K_Sty_A01_49084 (tab) MYNAH_p_Affy_plate_9_Mapping250K_Sty_A01_49084 Call
The rest of the SNP file contains one row of data for each probe, including the raw copy number value and the SNP calls generated by SNP microarray scanning software (such as Affymetrix's GeneChip software). Some modules, such as the SNPViewer module, require the data sorted by chromosome and physical position.