Hi,

I am analyzing raw microarray data obtained using the Agilent system. When I was looking at the pre-analyzed results of the same data, I found that the two control samples were additive inverses of each other (-0.42, 0.42), thereby canceling each other to give a median log2FC of 0, but this trend was absent in the treatment samples.

This pattern made me want to compare the control samples across each other, and after performing eBayes, I observe that the standard deviation between the controls is 0.71, but after making individual contrasts, and using the eBayes fit yet again, I get all 62976 probes when I filter by log2FC of 2.

I want to know if there's any other method of analyzing 1 color Agilent data.

Thank you.