[BioC] Re: read.GenePix() function

Hua Weng hweng at bmb-fs1.biochem.okstate.edu
Wed Nov 5 18:35:16 MET 2003

Hi, Jean and everybody:

In read.GenePix() function, is there any way I can specify Background Standard Deviation for Cy5 and Cy3( such as B647 SD and B546 SD) in GPR files?

user.raw <- read.GenePix(fnames=NULL, path=".", name.Gf="F546 Median", name.Gb="B546 Median", name.Rf="F647 Median", name.Rb="B647 Median", name.W="Flags",layout=user.layout, gnames=user.gnames, targets=user.samples, skip=30)

I want to specify these two columns is because I want to write a function to filter spots whose RF and GF are less than RB+2*RBSD and GB+2*GBSD. Do you know an approach I can do that?

Thank you very much,
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