[BioC] removal of probes called "Absent"

Cei Abreu-Goodger cei at ebi.ac.uk
Thu Jul 8 12:54:44 CEST 2010


Hi Hernando,

try:

pvals <- assayData(rawcalls)[["se.exprs"]]


Cheers,

Cei

Hernando Martínez wrote:
> 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,
> 
> 
> 
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