[BioC] gcrma problem
James W. MacDonald
jmacdon at med.umich.edu
Tue Aug 12 18:47:16 CEST 2008
Hi Glyn,
You want makeProbePackage() in the matchprobes package (plus the
probe_tab file for your chip, which hopefully you got from Affy).
Best,
Jim
Glyn Bradley wrote:
> Hi all,
>
> I'm using a custom affy chip, I have made the cdf using makecdfenv,
> installed it using R CMD INSTALL ..., and I can use the package affy
> sucessfully to do rma normalisations etc, but when trying to carry out
> gcrma in with the package gcrma, I get :
>
> eset <- gcrma(Data)
> Adjusting for optical effect...Done.
> Computing affinities[1] "Checking to see if your internet connection
> works..."
> [1] "Environment XXXXXaprobe was not found in the Bioconductor repository."
> Error in get(probepackagename) : variable "XXXXXaprobe" was not found
>
>
> How can I make/ install a custom XXXXaprobe file
>
> anyone? Thanks in advance
>
> Glyn
>
>
> This message has been checked for viruses but the contents of an attachment
> may still contain software viruses, which could damage your computer
> system:
> you are advised to perform your own checks. Email communications with the
> University of Nottingham may be monitored as permitted by UK legislation.
>
> _______________________________________________
> Bioconductor mailing list
> 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
--
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662
More information about the Bioconductor
mailing list