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.

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