Hi, all I am working on mouse Exon arrays from Affy. Because there are probes with multiple hits on the genome, I screened out these probes and exons with only one probe and transcript clusters with one exon on the array. After that I created a CDF file as illustrated from this group. My problems is: when I checked the probe level expressions (not gene expression) , the average is about 4.5 , and the gene expression level ( not surprisingly) is about similar level. And the smallest probe level was about 1.1. I also used the CDF file I downloaded from aroma here, using the same program, I got the gene expression level around 6.2. That is about 1.7 fold change. and the results from the new CDF that I created was just too low. I can't figure it out why. Can anyone give me some suggestions and hints? Thanks
Sabrina --~--~---------~--~----~------------~-------~--~----~ When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
