1 Sep 2004 02:33
Re:Flagging spots (was: Bioconductor documentation
At 05:28 AM 1/09/2004, you wrote:
>The reason that we want to read in more columns is to create the
>flags. Some people think that spots should be flagged if (e.g.) mean(Rf)
>differs considerably from median(Rf), or the s.d. of one of these measures
>is large. Right now, they need to create the flags outside of Bioconductor.
I think you might want something like
myfun <- function(x) {
okred <- abs(x[,"F635 Median"]-x[,"F635 Mean"]) < 50
okgreen <- abs(x[,"F532 Median"]-x[,"F532 Mean"]) < 50
as.numeric(okgreen & okred)
}
RG <- read.maimages(files, source="genepix", wt.fun=myfun)
Then all the "bad" spots will get weight zero which, in limma, is
equivalent to flagging them out. You can proceed with
RG$printer <- getLayout(RG$genes)
RG <- backgroundCorrect(RG) # gives more correction options
MA <- normalizeWithinArrays(RG)
to do print-tip loess normalization in which the flagged spots have no
influence on the normalization.
Gordon
>--Naomi
>
>At 09:28 AM 8/31/2004 +1000, you wrote:
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