[BioC] grouping samples from distinct runs in limma

[James W. MacDonald]

Hi Edmund,

Edmund Chang wrote:
> Dear list,
> 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 
> each other.

You almost certainly will need to add an effect to your model to account 
for the two batches of chips. A very good example can be found here:

http://bioinf.wehi.edu.au/marray/jsm2005/lab5/lab5.html

Note that they are fitting an effect to account for the day that the 
chips were processed which would be analogous to what you need to do.

An alternative would be to fit a mixed model by using the block argument 
to lmFit().


> 
> 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 
> correlated?

A relatively easy way to check this would be to do a principal 
components analysis and plot the first two PCs (you can use plotPCA() in 
affycoretools to do so). If the separate batches are grouping together, 
this gives you some assurance that there isn't a batch effect. 
Personally, I would err on the side of caution and assume that you need 
to do something to account for differences between the batches.

HTH,

Jim


> 
> or is there another function in limma that can handle this scenario?
> 
> Any input will be highly appreciated!
> Edmund Chang
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623