[BioC] LIMMA P-value calculations/Suggestions for flagged data

[Lance E. Palmer]

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