Entering edit mode
> Date: Wed, 21 Mar 2007 16:04:31 -0400
> From: "Lance E. Palmer" <lance.palmer at="" stonybrook.edu="">
> Subject: [BioC] LIMMA P-value calculations/Suggestions for flagged
> data
> To: bioconductor at stat.math.ethz.ch
>
> 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?
Yes, it is correct. If there is only one data value with weight>0 for
a particular probe, then
limma uses the empirical Bayes prior standard deviation for that probe
to form a t-statistic.
Think of it this way. You observed M=-3.765 for this probe. That's a
large negative value. You
know from looking at the other probes that the standard deviation of
M-values is usually around
0.03, say, so -3.7 is very likely genuinely different from zero.
> 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.
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.
Best wishes
Gordon
> However, the case above tells us something about the experiments.
How
> do people deal with this situation?
>
> -Lance Palmer
