[BioC] Extract M values from probes set to cluster

[J.Oosting at lumc.nl]

First of all, you will have to get rid of the missing values in your
selection vector

 selected[is.na(selected)]<-FALSE

Secondly, I think that you have duplicate spots on your array, with a
total of 6912 spots. It depends on the layout on the chip how you can
get to the M-values of both spots using the selected vector.
unwrapdups() can help you here
Something like this (untested) 
M.uw<-unwrapdups(MA.2$M,ndups=2,spacing=1) # ndups and spacing same as
in lmFit() and duplicateCorrelation()
M.ag<-apply(M.uw,1,function(x) (x[c(T,F)]+x[c(F,T)])/2)  # doesn't
handle NA
MA.selected<-M.ag[selected,]

Jan

 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Marcelo
Laia
Sent: dinsdag 13 februari 2007 12:51
To: Bioconductor
Subject: Re: [BioC] Extract M values from probes set to cluster

Dear Sean

I thought that I did a mistake in selected. Then, I try... But no
success.

Here are the outputs:

> selected  <- p.adjust(fit.2$p.value) <0.05
> summary(selected)
Mode   FALSE    TRUE    NA's
logical    2565     130     761
> length(selected)
[1] 3456
> MA.selected <- MA.2$M[selected, ]
> dim(MA.selected)
[1] 1782    3

I thought that I did a mistake here:

> selected  <- p.adjust(fit.2$p.value) <0.05
                      ^^^^^^^^^^

> selected  <- (fit.2$p.value) <0.05
> length(selected)
[1] 3456
> MA.selected <- MA.2$M[selected, ]
> dim(MA.selected)
[1] 4154    3
> fit.2 <- eBayes(fit)

Thank you very much

Laia