Hallo,

I'm using for the first time the limma package to analyse my array data, but both Bioconductor and limma are quite new for me.
I would like to weight the quality of the spots before analyse them.
At the moment I'm able to weigth the spot using their flags; before reading the output files of ImaGene (the software I used for image analysis), I set up that function:

> myfun <- function(x) as.numeric ( x$Flag <= 0 )

and than I read my data using:

> RG<-read.maimages(files,source="imagene",wt.fun=myfun)

I think in this way I should read the data only if the spots have flag=0...Is it correct?

What I would like to do is filtering the data, reading just the data respecting the following condition:

Signal Mean - Background Mean >2*Background Stdev 

Unfortunately I'm not able to write the code for that...

Could someone help my, please?

Thannk you!!!

Laura





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