Dear Mick,
The code I used is
targets <- readTargets("target.txt")
>
> #The QC filter
> myfun <- function(x,threshold=55){
> + okred <- abs(x[,"% > B635+2SD"]) > threshold
> + okgreen <- abs(x[,"% > B532+2SD"]) > threshold
> + okflag <- abs(x[,"Flags"]) > 0
> + okRGN <- abs(x[,"Rgn R˛"]) > 0.6
> + as.numeric(okgreen || okred || okflag || okRGN)
> + }
#End of QC filter
> RG_7 <- read.maimages(targets$FileName,
> source="genepix",wt.fun=myfun
> RG_7 <- read.maimages(targets$FileName,
> source="genepix",wt.fun=myfun)
> RG_7$genes <- readGAL()
(Gordon Smyth asked me nnot to use this step but the
normalizeWithinarrays() function does not work without
this step.)
> RG_7$printer <- getLayout(RG_7$genes)
> MA_7 <- normalizeWithinArrays(RG_7,method="loess")
> MA_7 <- normalizeBetweenArrays(MA_7)
> fit_7 <- lmFit(MA_7, design=c(1,-1,1,-1))
> fit_7 <- eBayes(fit_7)
> options(digits=3)
> Resultfile_7 <- topTable(fit_7, n=39000,
> adjust="fdr")
> Resdat_7 <-data.frame(Resultfile_7)
> write.table(Resdat_7,file='Result.csv',quote =
FALSE,
> sep = "\t")
The NA
I wrote a perl program to get a set of genes using the
alpha value as 0.05.
-Ankit
--- "michael watson (IAH-C)"
<michael.watson@bbsrc.ac.uk> wrote:
> Ankit
>
> Can you please include some sample code so we can
> figure out exactly
> what it is you are doing?
>
> Many thanks
> Mick
>
> -----Original Message-----
> From: bioconductor-bounces@stat.math.ethz.ch
> [mailto:bioconductor-bounces@stat.math.ethz.ch] On
> Behalf Of Ankit Pal
> Sent: 18 May 2005 10:12
> To: bioconductor@stat.math.ethz.ch
> Subject: [BioC] NA instead of block row and ID and
> column values
>
>
> Dear All,
> Please ignore my previous query titled "The meaning
> of
> NA in all the result summary".
> I am reframing my question.
> I am using a set of gpr files for analysis with the
> LIMMA package.
> On completion of the analysis, I get a set of 2000
> genes with p value< 0.05.
> There are some spots in this file which contain the
> M,
> A, T, p and B values but in the fields named Block
> row
> column and ID there is an "NA". (See attachment)
> The block, row, column and ID values are inherited
> from the GPR files and are present in the same. So
> why
> did LIMMA replace them with a "NA"?
> In the total set of 30010 genes, 7270 have NA's in
> them, which is not the case in the corresponding gpr
> file.
> Is this because the NA represents spots that did not
> get through the spot filtering step?
> Looking forward to a reply,
> thank you,
> -Ankit
>
>
>
> __________________________________
>
>
>
