[BioC] Limma analysis

Gordon Smyth smyth at wehi.edu.au
Tue Oct 28 03:50:49 MET 2003

At 10:04 AM 28/10/2003, Pete wrote:
>Hi all,
>I have been using limma now for a couple of weeks, and I think I have pretty
>much got the hang of most of it. However, now I want to analyse a slightly
>more complex experiment, can anyone give me some guidance as how to deal
>with this.
>      Firstly the experimental design is as follows, there are four samples
>wildtype tissue A, wildtype tissue B, mutant tissue A and mutant tissue B.
>Each sample has been compared to eachother in triplicate (inlcuding a dye
>swap, and one independant sample). To complicate things further an
>additional set of WT A v WT B was also done in triplicate using a different
>     The slides are 7.5k oligos spotted in duplicate ( the duplicates are in
>the same block 10 rows below the first copy), although there are control
>genes which appear more than twice on the arrays. My files are imagene
>output files where the cy5 and cy3 are contained in separate files.  Also
>the imagene output contains spots which are flagged and would need to be
>removed from the analysis (meaning that a particular gene could have none
>one or two measurements for it).
>What do you think the best strategy to deal with this design is?

Well, everything in your experiment is straight down the line as far as 
limma is concerned. You haven't really said what is is about this 
experiment which you're not sure how to deal with. Is the problem the 
design matrix or something else?



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