[BioC] [limma] Unreliable spots - omitting in avereps

[mjonczyk]

Dear List,

I have question about using weights, avereps and lmFit in limma.

I've set weights for each spot using Flags from GenePix files.
Then I normalized data and removed control spots.

Next I want to replace row IDs (probe IDs) with genes IDs -- sometimes 
more than one probe corresponds to the same gene

i.e. MZ0001 = GRMZ0001
      MZ0004 = GRMZ0001

so I used avereps function to average data for rows for the same genes.

The problem is that avereps averages also weights -- if MZ0001 has "0" 
weight
and MZ0004 "1" weight, gene GRMZ0001 has weight "0.5" so it is used in 
lmFit, eBayes and so on.
It is not desirable as one of the spots are unreliable (Bad in GenePix 
= weight "0").

I have an idea not to use spots with weight 0 when I compute averages.
So, using above example, GRMZ0001 will have the same value as MZ0004 
(which has 1 weight).

Unfortunately my skills are not so high to allow me do it.
Could anyone give me any hint how can I do it?

Best wishes,
Maciej Jończyk
-- 
Maciej Jonczyk,
Department of Plant Molecular Ecophysiology
Faculty of Biology, University of Warsaw
02-096 Warsaw, Miecznikowa 1
Poland



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