Hi, all, When I ran my old chip data (RN U34 chips) with gcrma, I got the following error. I had no problem with other chip types. Can someone give me some inputs on this? Thank you. > gcrma.ob<-gcrma(ob) Computing affinitiesError in get(x, envir, mode, inherits) : variable "rnu34probe" was not found I am using R 2.0.1 and gcrma 1.1.3. Best, Puhong [[alternative HTML version deleted]]

Please check the probepackage name and cdfpackage name for your chip type first. The ones provided on bioconductor usually have names like "CHIPcdf" and "CHIPprobe" where CHIP is the chip type such as "hgu133a". If your probe package is created with a name following different convention, gcrma may not recognize it. On Tue, 10 May 2005, Puhong Gao wrote: > Hi, all, > > When I ran my old chip data (RN U34 chips) with gcrma, I got the following error. I had no problem with other chip types. Can someone give me some inputs on this? Thank you. > > > gcrma.ob<-gcrma(ob) > Computing affinitiesError in get(x, envir, mode, inherits) : variable "rnu34probe" was not found > > I am using R 2.0.1 and gcrma 1.1.3. > > Best, > > Puhong > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Puhong Gao wrote: > Hi, all, > > When I ran my old chip data (RN U34 chips) with gcrma, I got the following error. I had no problem with other chip types. Can someone give me some inputs on this? Thank you. > > >>gcrma.ob<-gcrma(ob) > > Computing affinitiesError in get(x, envir, mode, inherits) : variable "rnu34probe" was not found With the version of gcrma you are using, you should not be able to get to that point without automagically installing the correct probe package. How about trying library(reposTools) install.packages2("rnu34probe") and then run gcrma() again. Best, Jim > > I am using R 2.0.1 and gcrma 1.1.3. > > Best, > > Puhong > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

Hi, Zhijin and Jim, Thank you both for your quick input. Indeed, R automatically initiated the installation of "rnu34cdf" and "rnu34probe" when I first ran GCRMA. Since I got the posted error, I manually installed rnu34 packages downloaded from Bioconductor site and got the same error when GCRMA was run. I did check the package names and found no problem. By the way, I ran GCRMA on rgu34a chip data without problem yesterday. Is there anything else I should check? Thank you. Best, Puhong ----- Original Message ----- From: "Zhijin Wu" <zwu@jhsph.edu> To: "Puhong Gao" <pgao@hunter.cuny.edu> Cc: <bioconductor@stat.math.ethz.ch> Sent: Tuesday, May 10, 2005 3:00 PM Subject: Re: [BioC] GCRMA error > Please check the probepackage name and cdfpackage name for your chip type > first. > The ones provided on bioconductor usually have names like > "CHIPcdf" and "CHIPprobe" where CHIP is the chip type such as "hgu133a". > If your probe package is created with a name following different > convention, gcrma may not recognize it. > > > On Tue, 10 May 2005, Puhong Gao wrote: > >> Hi, all, >> >> When I ran my old chip data (RN U34 chips) with gcrma, I got the >> following error. I had no problem with other chip types. Can someone give >> me some inputs on this? Thank you. >> >> > gcrma.ob<-gcrma(ob) >> Computing affinitiesError in get(x, envir, mode, inherits) : variable >> "rnu34probe" was not found >> >> I am using R 2.0.1 and gcrma 1.1.3. >> >> Best, >> >> Puhong >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >>

Hi, Zhijin, I don't see "rnu34probe" and other chip packages (see below) > search() [1] ".GlobalEnv" "package:splines" "package:gcrma" [4] "package:matchprobes" "package:affy" "package:reposTools" [7] "package:Biobase" "package:tools" "package:methods" [10] "package:stats" "package:graphics" "package:grDevices" [13] "package:utils" "package:datasets" "Autoloads" [16] "package:base" > I just tried GCRMA on RG U34a data and it worked without a problem (see below). (R was started in a different folder, if it means anything.). So, it should be rnu34 chip specific. > local({pkg <- select.list(sort(.packages(all.available = TRUE))) + if(nchar(pkg)) library(pkg, character.only=TRUE)}) Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: reposTools Loading required package: matchprobes > search() [1] ".GlobalEnv" "package:gcrma" "package:matchprobes" [4] "package:affy" "package:reposTools" "package:Biobase" [7] "package:tools" "package:methods" "package:stats" [10] "package:graphics" "package:grDevices" "package:utils" [13] "package:datasets" "Autoloads" "package:base" > g.so<-gcrma(so) Computing affinities.Done. Adjusting for optical effect..............................Done. Adjusting for non-specific binding..............................Done. Normalizing Calculating Expression > Best, Puhong ----- Original Message ----- From: "Zhijin Wu" <zwu@jhsph.edu> To: "Puhong Gao" <pgao@hunter.cuny.edu> Cc: <bioconductor@stat.math.ethz.ch> Sent: Tuesday, May 10, 2005 5:15 PM Subject: Re: [BioC] GCRMA error > Do you see "rnu34probe" when you do > > search() > > If yes, what do you get if you do > > P <-get("rnu34probe") >