[BioC] tech reps revisited in limma

Naomi Altman naomi at stat.psu.edu
Mon May 17 01:33:05 CEST 2004

The simplest thing to do is to average the technical reps 
afternormalization but before running limma.


At 04:40 PM 5/2/2004, Simon Melov wrote:
>After viewing the various postings on this topic ("technical replicates 
>(again!): a summary"), I couldnt find a solution to a pretty basic 
>problem. I have two technical replicates per sample, and 7 samples per 
>treatment. I have 4 treatments, which I want to contrast with each other 
>(all using 2-color chemistry).
>I created a design which treated each sample as a duplicate (i..e 1, -1 as 
>dye swaps were involved), and then tried to use this to create contrasts, 
>with subsetting etc. This ended up being very laborious, and there may not 
>be a way to do this easily in limma, but I could be missing something.
>What I have is this: 4 treatments: A,B,C,D
>For each treatment, I have 2 technical replicates  (dye swaps), I want to 
>average these in limma, and then look at comparisons between groups, and 
>create contrasts between A and B, etc. However, I dont see an easy way of 
>doing this, short of a lot of subsetting, and renaming variables.
>Any help would be appreciated.
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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