Hi.
I have test and control samples obtained from different chip file.
Test is obtain from u133a2 file and control is from HuGene 2-0.1v2
There are 76 treated samples (u133a2)and 2 control samples(HuGene chip)
I want to perform all 76 with 2 control Gene expression analysis using package like affy and limma .
How can I do this type of analysis.
I agree that the two samples have different probeset.
But I don't know how to deal with such data.
Please help me