[BioC] Reference individual array in abatch after changing pData

[Paul Geeleher]

Hi thanks for your reply, but I've actually worked out that this
problem was to do with the fact that i was running an older version of
Bioconductor. Version 2.5.1. Upgrading has solved it. Sorry for
wasting your time.

-Paul

On Mon, Apr 7, 2008 at 8:40 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> 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
>  1100 Fairview Ave. N.
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>
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