[BioC] extract intensity values from AffyBatch

[James W. MacDonald]

Hi Assa,

On 5/18/2011 3:46 AM, Assa Yeroslaviz wrote:
> Hi,
>
> I'm trying to extract a matrix of intensity values from an AffyBatch object.
>
> I know I can have them using
>> Intensity(AffyBatch)
> or
>> exprs(AffyBatch)
>
> but I would like to have a full matrix with the probe names.
> Unfortunately I can't find a way of doing it.

There isn't IIRC a direct way of doing this. Here is an example of one 
way using the Dilution dataset.

 > library(affydata)
 > data(Dilution)
 > pms <- pm(Dilution, LISTRUE=TRUE)
 > for(i in names(pms)) row.names(pms[[i]]) <- rep(i, nrow(pms[[i]]))
 > pms2 <- do.call("rbind", pms)
 > head(pms2)
             20A   20B 10A   10B
100_g_at  221.3 146.3 192 116.0
100_g_at  685.0 479.0 493 328.3
100_g_at 1126.3 724.3 849 498.3
100_g_at  205.0 126.5 136  97.0
100_g_at  580.8 341.8 374 226.0
100_g_at  161.3 109.5 139  92.3

You can do the analogous thing for MM probes using the mm() function.

Best,

Jim


>
> There are several way of extracting the names of the probes, but not in the
> same order or magnitude compared to the intensity array.
>
>> length(geneNames(rawData))[1] 18952>  length(probeNames(rawData))[1] 265358>  dim(intensity(rawData))[1] 535824     12>  dim(exprs(rawData))[1] 535824     12
>
> Does anyone has an idea of how to extract these Values into a matrix. I have
> the original CEL files.
>
> Even a way outside of R will be welcome.
>
> Thanks
>
> Assa
>
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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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