[BioC] grouping samples from distinct runs in limma
echang4 at life.uiuc.edu
Thu Mar 2 05:49:16 CET 2006
I am working with Affymetrix microarrays and looking for differential
gene expression using limma. We repeated the same microarray experiment
two separate times (about a year apart), because *some* of the
microarrays came out bad. So instead of running the same samples again
(technical replicates), we generated an entirely new set of RNA.
(i.e. for treatment A: 1st run- A1, A2, A3; 2nd run- a1, a2, a3)
(and for treatment B: 1st run- B1,B2,B3; 2nd run- b1,b2,b3)
I was wondering how to handle this sort of data in limma. Because they
are biologically distinct, I am tempted to group them together (e.g.
combining samples A1,A2,A3 and a1, a2, a3 into A1-A6). But I have
reservations about grouping arrays which were run one year apart from
How can I prove to myself that samples which were identically treated
but came from separate experiments can be grouped together in limma? Do
I calculate the correlation coefficient between groups
(corfit$consensus) and use that to determine if the groups are closely
or is there another function in limma that can handle this scenario?
Any input will be highly appreciated!
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