[BioC] help needed

[Ozge Gursoy-Yuzugulu]

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