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).
CN File Format
This is a tab-delimited file format that contains SNP copy numbers. It contains one row for each SNP and one column for each SNP array: the raw copy number 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_N_name)
SNP (tab) Chromosome (tab) PhysicalPosition (tab) MYNAH_p_Affy_plate_9_Mapping250K_Sty_A01_49068 (tab) ... MYNAH_p_Affy_plate_9_Mapping250K_Sty_A01_49084
The rest of the SNP file contains one row of data for each SNP.