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

Peng Yu pengyu.ut at gmail.com
Wed Jul 22 22:08:19 CEST 2009


Hi,

I am still new to bioc. Could you please point me the most relevant
document? Shall I start with the following document?

http://www.bioconductor.org/packages/release/bioc/vignettes/oligo/inst/doc/oligoNimblegenExpression.pdf

Regards,
Peng

On Wed, Jul 22, 2009 at 1:43 PM, Vincent Carey
<stvjc at channing.harvard.edu> wrote:
>
> 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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> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
> --
> Vincent Carey, PhD
> Biostatistics, Channing Lab
> 617 525 2265



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