[BioC] Eliminating Absent Data

[James W. MacDonald]

Hi Supriya,

On 5/19/2011 3:39 PM, Supriya Munshaw wrote:
> Hi all,
>
> I have
>
> 1.       an affy object that contains all my normalized data, the
> result from rma.
>
> 2.       an affy object that contains P/M/A calls, the result from
> mas5calls.
>
> I now want to eliminate probe sets from my normalized data that are
> absent in all my samples. I then want to set up a contrast matrix and
> fit a model using probesets that are only present in ALL samples.
>
> Does anyone know how I can extract this subset of data from my object
> in 1?

Let's say your ExpressionSet containing the mas5calls is called 
'mcalls', and the ExpressionSet containing the rma data is called 'eset'.

ind <- apply(exprs(mcalls), 1, function(x) all(x == "A"))
filteredEset <- eset[!ind,]

Best,

Jim


>
> Thanks!
>
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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