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, Hua [[alternative HTML version deleted]]

Hi Hua, There is no ready made function for this at the moment. I will suggest you modified version of the function "read.marrayRaw", and read the extra two columns of values per slide. If you like further help with that, let me know. Cheers Jean > 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?