[BioC] removal of probes called "Absent"

[Iain Gallagher]

HI Hernando

Is this any use:

#get rid of absent probes
dataIn <- ReadAffy()

masData <- mas5(dataIn)

calls <- mas5calls(dataIn)

calls <- exprs(calls)

absent <- rowSums(calls == 'A')

absent <- which (absent == ncol(calls))

dataFiltered <- masData[-absent,]

iain

--- On Thu, 8/7/10, Hernando Martínez <hernybiotec at gmail.com> wrote:

> From: Hernando Martínez <hernybiotec at gmail.com>
> Subject: [BioC] removal of probes called "Absent"
> To: Bioconductor at stat.math.ethz.ch
> Date: Thursday, 8 July, 2010, 11:48
> Hi, I am trying to remove probes
> called A (absent) in all my microarray
> samples.
> I am trying to get the p-values for the probes across all
> samples so I can
> use genefilter to create a mask and select the present
> genes. However, I get
> the following error:
> 
> > data<-ReadAffy()
> > rawcalls<-mas5calls(data)
> Getting probe level data...
> Computing p-values
> Making P/M/A Calls
> > se.exprs(rawcalls)
> Error in function (classes, fdef, mtable)  :
>   unable to find an inherited method for function
> "se.exprs", for signature
> "ExpressionSet"
> 
> se.exprs is supposed to give me the p.values, isn't it?
> 
> Help is much appreciated, thanks,
> 
> -- 
> Hernando Martínez Vergara
> 
>     [[alternative HTML version deleted]]
> 
> 
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