Hi could someone give me an example of how to use the spot quality (name.W) option from marrayRaw, I have a marrayRaw object with name.W taken from a flags column from genepix (gpr) files but I'm not sure how to use it to discard data in subsequent normalisations. The gpr files have either P (pass), M (marginal) F (fail) OR 0,-50 and -100 respectively. Can you do this in R as well as bioconductor ? for data that isn't marrayRaw cheers Jason

Hi Jason, At 08:10 PM 2/06/2003, Jason Skelton wrote: >Hi > >could someone give me an example of how to use the spot quality (name.W) >option from marrayRaw, I have a marrayRaw object with name.W taken from a >flags column from genepix (gpr) files but I'm not sure how to use it to >discard data in subsequent normalisations. The gpr files have either P >(pass), M (marginal) F (fail) OR 0,-50 and -100 respectively. I'd encourage you to persevere with marrayRaw. I am sure that what you want to do can be done with maNormMain. >Can you do this in R as well as bioconductor ? >for data that isn't marrayRaw Well, an alternative is to use the limma package, which is designed to make it easy to use spot quality weights. If 'files' is a character vector containing the names of the GenPix gpr files, you want to give zero weight to the non-passing spots, and your gal file is in your working directory, then you can type library(limma) gal <- readGAL() RG <- read.maimages(files, source="genepix", wt.fun=wtflags(0)) MA <- normalizeWithinArrays(RG, getLayout(gal)) This will perform print-tip group loess normalization giving zero weight to all spots which GenePix gives a negative flag. I think I'd probably use wt.fun=wtflags(0.1) or similar which gives 10% weight to the non- passing spots, just to keep them in the normalizing regressions. Cheers Gordon >cheers > >Jason