[BioC] help needed

[Sean Davis]

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