To whom it may concern,

I've been having some problems with consistency in my limma results for
genes that are found to have significant differential transcript abundance.

In a given example, I may have 4 different groups (a, b, c, and d) in an
array set of 12.

>From here, I make a contrast matrix that has contrasts for a-b, a-c, and
a-d.  Eventually, I output an eBaye's corrected contrast fit and I use
decideTests from there to find out what genes are differentially expressed.
My misunderstanding is that when I take away an entire group (such as
removing all d's) and redo all steps in the limma analysis, I find that I
end up with a different set of genes after using decideTests.  I am confused
here, because I would not think that removing group 'd' from the analysis
would have an effect on contrasts a-b and a-c.

If anyone could even hint to me a reason as to why this is happening, it
would be greatly appreciated.

Thanks and regards,
Joseph Skaf



-- 
Joseph Skaf
PhD student

Department of Cell and Systems Biology
University of Toronto
25 Willcocks Street
Toronto, Ontario M5S 3B3

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