I just had a question/concern about P value calculations in Limma (I am using latest version of Bioconductor) I recently ran 3 arrays through my analysis. The slides were analayzed with Genepix software. There were a couple of genes that concerned me. One had a log fold change of -3.765. The adjusted p-value (fdr) was .027. I looked at the individual M values for the arrays and they were -0.009336, 0.09217 and -3.765. I noticed that the first two arrays had a 'not found' flag. So basically the analysis gave a significant P-value using only 1 piece of data. Is this something that is correct? I also wonder if I should even remove 'not found' flagged data. Originally I did not, but someone suggested I do. I originally did not remove it because of the case listed above. However, the case above tells us something about the experiments. How do people deal with this situation? -Lance Palmer

> I've argued on this mailing list and elsewhere for a long time that, > rather than flagging faint > spots, it's better to use a better background correction method that > avoids a blow out of M-values > at low intensities. Is RMA such a good background correction method? cheers, sergio