[BioC] Reference individual array in abatch after changing pData

[Martin Morgan]

Hi Paul -- can you please provide the output of sessionInfo() ?

Thanks,

Martin

"Paul Geeleher" <paulgeeleher at gmail.com> writes:

> Dear Memebers,
>
> I want to be able to reference individual arrays in an abatch like so
> abatch[,1], abatch[,2] etc.
>
> This seems to work fine using the original pData for the abatch after
> using ReadAffy():
>
>                   sample
> N10S.CEL      1
> N11S.CEL      2
> N12S.CEL      3
> N7S.CEL       4
> N8S.CEL       5
> N9S.CEL       6
> P1S.CEL       7
> P2S.CEL       8
> P3S.CEL       9
> P4S.CEL      10
> P5S.CEL      11
> P6S.CEL      12
>
>
> But when I run these commands:
>
> pd <- data.frame(population = c(1,1,1,1,1,1,2,2,2,2,2,2), replicate =
> c(1,2,3,4,5,6,1,2,3,4,5,6), sample = c(1,2,3,4,5,6,7,8,9,10,11,12))
> rownames(pd) <- sampleNames(abatch)
> pData(abatch) <- pd
>
> Which changes the pData for the abatch to this:
>
>          population replicate sample
> N10S.CEL          1         1      1
> N11S.CEL          1         2      2
> N12S.CEL          1         3      3
> N7S.CEL           1         4      4
> N8S.CEL           1         5      5
> N9S.CEL           1         6      6
> P1S.CEL           2         1      7
> P2S.CEL           2         2      8
> P3S.CEL           2         3      9
> P4S.CEL           2         4     10
> P5S.CEL           2         5     11
> P6S.CEL           2         6     12
>
> Referencing the arrays using "abatch[,1]" throws up the following error:
>
> Error in `row.names<-.data.frame`(`*tmp*`, value = c("sample", "population",  :
>         invalid 'row.names' length
>
>
> How can I change the pData and still be able to reference the arrays
> like "abatch[,1]"?
>
> Thanks,
> -Paul
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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