[BioC] removal of probes called "Absent"
Iain Gallagher
iaingallagher at btopenworld.com
Thu Jul 8 15:35:35 CEST 2010
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]]
>
>
> -----Inline Attachment Follows-----
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
More information about the Bioconductor
mailing list