[BioC] Error "Specified environment does not contain MoGene-1_0-st-v1"

[Vincent Carey]

you'll need to use the oligo package to work with that data.

    source("http://bioconductor.org/biocLite.R")
    biocLite("oligo", "pd.mogene.1.0.st.v1")

then oligo's read.celfiles() and rma() can be used.  you may also need

biocLite("mogene10stprobeset.db")

to help interpret results

On Wed, Jul 22, 2009 at 2:37 PM, Peng Yu <pengyu.ut at gmail.com> wrote:
>
> Hi,
>
> I have some .cel files and MoGene-1_0-st-v1,r3.cdf in the current
> directory. The .cel files are generated from the Mouse Gene 1.0 ST
> Array.
>
> I run the following command. But it generate an error message. Can
> somebody let me know what the problem is?
>
> Regards,
> Peng
>
> > setwd(".")
> > library(makecdfenv)
> > data<-ReadAffy()
> > eset<-rma(data)
> Error in getCdfInfo(object) :
>   Could not obtain CDF environment, problems encountered:
> Specified environment does not contain MoGene-1_0-st-v1
> Library - package mogene10stv1cdf not installed
> Bioconductor - mogene10stv1cdf not available
>
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--
Vincent Carey, PhD
Biostatistics, Channing Lab
617 525 2265