[BioC] Extract M values from probes set to cluster

[Marcelo Laia]

Hi Jan,

I try your suggestion and some errors appear.

Could you (or someone) help me again?

Thank you very much

> fit.2 <- eBayes(fit)
> selected  <- (fit.2$p.value) <0.05
>
> selected[is.na(selected)]<-FALSE
>
> MA.selected <- MA.2$M[selected, ]
>
> M.uw<-unwrapdups(MA.2$M,ndups=2,spacing=32)
>
> M.ag<-apply(M.uw,1,function(x) (x[c(T,F)]+x[c(F,T)])/2)
>
> MA.selected<-M.ag[selected,]
Error: (subscript) logical subscript too long
> length(selected)
[1] 3456
> length(M.uw)
[1] 20736
> length(M.ag)
[1] 10368
> dim(MA.selected)
[1] 2632    3
> dim(M.uw)
[1] 3456    6
> dim(M.ag)
[1]    3 3456
>

Marcelo

2007/2/13, J.Oosting at lumc.nl <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
>


-- 
Marcelo Luiz de Laia
Ph.D Candidate
São Paulo State University (http://www.unesp.br/eng/)
School of Agricultural and Veterinary Sciences
Department of  Technology
Via de Acesso Prof. Paulo Donato Castellane s/n
14884-900   Jaboticabal - SP - Brazil
Phone: +55-016-3209-2675
Cell: +55-016-97098526