Hello, I am working on two isogenic cell lines that I compare their response to selenium deficiency. I provided RNA to a company to do my affy arrays. I recently got CEL files. After applying two different R test I observe that there is only 4-5 probes with a P value less than 0.05 which is impossible since the phenotypes of these two sets of data. I wonder if anyone knows any R method to assess if the company somehow mixed my samples and used. Thanks Ozge

Ozge Gursoy-Yuzugulu wrote: > Hello, > I am working on two isogenic cell lines that I compare their response > to selenium deficiency. I provided RNA to a company to do my affy > arrays. I recently got CEL files. > After applying two different R test I observe that there is only 4-5 > probes with a P value less than 0.05 which is impossible since the > phenotypes of these two sets of data. I wonder if anyone knows any R > method to assess if the company somehow mixed my samples and used. > Have you looked specifically at the quality of the data? Also, a simple hierarchical clustering should show you the overall structure of your data. Sean