Extract subset of data file

[Analysis example, Version 9/28/06+] Here we show how to extract a subset of data from a larger data file, with possible reordering of rows and columns. This can be useful when subsetting 500K Hapmap genotype calls to make a reference call file for LOH inference. First use "Get external data" to read in "Sty_HapMap270_brlmm_call.txt" (uncheck "Has both signal and call" and check "SNP data"), then specify an array list file containing 60 CEPH parent samples. Then go to "Tools/Export expression data", select all samples and specify a probe set list file with the same ordering as probe sets in CDF or genome information file. Affymetrix library files contain a PSI file (example, unzip it), which can be used as probe set list file (but check "Use probe set name in the 2nd column"). Uncheck "Has both signal and call" if making reference genotype file. The exported file can then be used as "Analysis/Chromosome/Options/Reference genotype file".