[BioC] limma Normalization question

[Gordon Smyth]

>[BioC] limma Normalization question
>Cecilia McGregor cmcgre1 at lsu.edu
>Tue Nov 22 00:54:53 CET 2005
>
>Dr Smyth
>
>I have some control spots that are not differentially expressed on the array.
>I tried to use the modifyWeights as on page 21 of the Users Guide (6 Oct 
>2005).
>However I realized that it doesn't work, cause I don't use weights in my
>read.maimages. I used a image analysis program, not recognized by limma, 
>so used
>the following to read the data.
>
>RG <- read.maimages(targets$FileName, 
>columns=list(R="Rf",G="Gf",Rb="Rb",Gb="Gb"))
>
>I tried to add "phony" column for weights (all values=1) in the intensity 
>files,
>so I can modify it, but have not been able to get it to work (yet).
>
>Cecilia

Dear Cecilia,

There's no need to change the data files (a last resort!), you could just 
use for example

RG$weights <- array(1, dim(RG))

Best wishes
Gordon