We had a discussion in our lab about false discovery rate correction.  Most people felt a little disappointed with their microarray data after in many cases a long hard slog with the lab process.  The FDR (BY, BH etc. etc.) knocked their un-adjusted gene lists into very,very short lists of differentially expressed genes.  I work on disease pathology and thought microarrays would provide me with a constellation of clues.  Instead I find for some time periods I have none.  This is with a 17,500 cDNA custom chip.

It surprised me that many knew of papers published without applying an FDR adjustment.  I had just assumed that for a proper statistical analysis had to have one.

I wonder what people are doing regarding using/not using an FDR?

What FDR corrections are people using?

What newer alternatives are there that are less conservative?

Sally Goldes
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