gcrma()/rma() error
1
0
Entering edit mode
@michael-seewald-574
Last seen 10.2 years ago
Dear Bioconductor people, dear Jean and Rafael, I see the same problem as Jose described (see below) with justGCRMA(). The following (while located in a directory with CEL files) does not work: > DATA.A.GCRMA<-justGCRMA(phenoData=pd) Computing affinities..Done. Adjusting for optical effect......................Done. Adjusting for non-specific binding.....................Done. Normalizing Calculating Expression Error in just.gcrma(filenames = filenames, phenoData = phenoData, description = description, : dimnames applied to non-array Splitting the task into two commands works: > DATA.A.GCRMA<-justGCRMA() Computing affinities..Done. Adjusting for optical effect......................Done. Adjusting for non-specific binding.....................Done. Normalizing Calculating Expression > phenoData(DATA.A.GCRMA) <- pd There seems to be a (non-critical) bug hidden in the code for the phenotypic data. By the way, doing the same with justRMA in one step works fine. Do you need more information for debugging? Regards & best wishes, Michael On Tue, 6 Apr 2004, Jose Duarte wrote: > Hi all > > I've got the file test.R with the following code: > > filenames <- c("1M2W050304.CEL", "2M2W050304.CEL", "3M2W050304.CEL", > "1M1W050304.CEL", "1M3W050304.CEL") > filepath <- "/net/array/WormDystrophy" > samples <- c("1M2W050304.CEL", "2M2W050304.CEL", "3M2W050304.CEL", > "1M1W050304.CEL", "1M3W050304.CEL") > custom <- c("rma", "quantiles", "pmonly", "medianpolish") > log2trans <- TRUE > library(affy) > library(gcrma) > library(vsn) > bgcorrect.methods <- c(bgcorrect.methods, "gcrma") > normalize.AffyBatch.methods <- c(normalize.AffyBatch.methods, "vsn") > express.summary.stat.methods <- c(express.summary.stat.methods, "rlm") > setwd(filepath) > exprset <- rma(ReadAffy(filenames = filenames)) > > > > I run it in batch mode from the linux command line with "R --no-save < > test.R". Everything is ok, except when executing the last line. The > rma() runs fine with the usual output: > > Background correcting > Normalizing > Calculating Expression > > But then it comes with the error: > > Error in rma(ReadAffy(filenames = filenames)) : > dimnames applied to non-array > Execution halted > > > > This is REALLY weird because: > > 1) It runs well in an interactive session just by copying and pasting > the code from the test.R file > > 2) It works fine if I change the order in which the file names are > given!! > > > Any ideas what the error means or what might be happening here? (I'm on > RedHat9, R 1.8.1, affy 1.3.28) > > Thanks > > Jose > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
affy affy • 1.1k views
ADD COMMENT
0
Entering edit mode
@michael-seewald-574
Last seen 10.2 years ago
Sorry, I have to correct myself. I just noted that the command fails *ONLY* in the non-interactive environemnt, e.g. when calling a script with "source". It works when I paste the command interactively into the R shell. This means it behaves exactly like Jose described.. Best wishes, Michael On Fri, 18 Jun 2004, Michael Seewald wrote: > > Dear Bioconductor people, dear Jean and Rafael, > > I see the same problem as Jose described (see below) with justGCRMA(). > > The following (while located in a directory with CEL files) does not work: > > > DATA.A.GCRMA<-justGCRMA(phenoData=pd) > Computing affinities..Done. > Adjusting for optical effect......................Done. > Adjusting for non-specific binding.....................Done. > Normalizing > Calculating Expression > Error in just.gcrma(filenames = filenames, phenoData = phenoData, description > = description, : > dimnames applied to non-array > > Splitting the task into two commands works: > > > DATA.A.GCRMA<-justGCRMA() > Computing affinities..Done. > Adjusting for optical effect......................Done. > Adjusting for non-specific binding.....................Done. > Normalizing > Calculating Expression > > phenoData(DATA.A.GCRMA) <- pd > > There seems to be a (non-critical) bug hidden in the code for the phenotypic > data. By the way, doing the same with justRMA in one step works fine. > > Do you need more information for debugging? > > Regards & best wishes, > Michael > > > On Tue, 6 Apr 2004, Jose Duarte wrote: > > > Hi all > > > > I've got the file test.R with the following code: > > > > filenames <- c("1M2W050304.CEL", "2M2W050304.CEL", "3M2W050304.CEL", > > "1M1W050304.CEL", "1M3W050304.CEL") > > filepath <- "/net/array/WormDystrophy" > > samples <- c("1M2W050304.CEL", "2M2W050304.CEL", "3M2W050304.CEL", > > "1M1W050304.CEL", "1M3W050304.CEL") > > custom <- c("rma", "quantiles", "pmonly", "medianpolish") > > log2trans <- TRUE > > library(affy) > > library(gcrma) > > library(vsn) > > bgcorrect.methods <- c(bgcorrect.methods, "gcrma") > > normalize.AffyBatch.methods <- c(normalize.AffyBatch.methods, "vsn") > > express.summary.stat.methods <- c(express.summary.stat.methods, "rlm") > > setwd(filepath) > > exprset <- rma(ReadAffy(filenames = filenames)) > > > > > > > > I run it in batch mode from the linux command line with "R --no- save < > > test.R". Everything is ok, except when executing the last line. The > > rma() runs fine with the usual output: > > > > Background correcting > > Normalizing > > Calculating Expression > > > > But then it comes with the error: > > > > Error in rma(ReadAffy(filenames = filenames)) : > > dimnames applied to non-array > > Execution halted > > > > > > > > This is REALLY weird because: > > > > 1) It runs well in an interactive session just by copying and pasting > > the code from the test.R file > > > > 2) It works fine if I change the order in which the file names are > > given!! > > > > > > Any ideas what the error means or what might be happening here? (I'm on > > RedHat9, R 1.8.1, affy 1.3.28) > > > > Thanks > > > > Jose > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > >
ADD COMMENT
0
Entering edit mode
It seems, I found the reason: When justGCRMA() is called in a subdirectory that contains the substring "GMS_AllLCM-133A_Foo" it does NOT work. When I rename it to "GMS_AllLCM-U133A_Foo" it runs fine. The "-" followed by a number is apparently interpreted in a special (numerical?) way when justGCRMA reads the CEL files from that directory. All of that applies only to the non-interactive session, it runs fine in the interactive session. Best regards, Michael On Fri, 18 Jun 2004, Michael Seewald wrote: > > Sorry, I have to correct myself. I just noted that the command fails *ONLY* in > the non-interactive environemnt, e.g. when calling a script with "source". It > works when I paste the command interactively into the R shell. This means it > behaves exactly like Jose described.. > > Best wishes, > Michael > > > On Fri, 18 Jun 2004, Michael Seewald wrote: > > > > > Dear Bioconductor people, dear Jean and Rafael, > > > > I see the same problem as Jose described (see below) with justGCRMA(). > > > > The following (while located in a directory with CEL files) does not work: > > > > > DATA.A.GCRMA<-justGCRMA(phenoData=pd) > > Computing affinities..Done. > > Adjusting for optical effect......................Done. > > Adjusting for non-specific binding.....................Done. > > Normalizing > > Calculating Expression > > Error in just.gcrma(filenames = filenames, phenoData = phenoData, description > > = description, : > > dimnames applied to non-array > > > > Splitting the task into two commands works: > > > > > DATA.A.GCRMA<-justGCRMA() > > Computing affinities..Done. > > Adjusting for optical effect......................Done. > > Adjusting for non-specific binding.....................Done. > > Normalizing > > Calculating Expression > > > phenoData(DATA.A.GCRMA) <- pd > > > > There seems to be a (non-critical) bug hidden in the code for the phenotypic > > data. By the way, doing the same with justRMA in one step works fine. > > > > Do you need more information for debugging? > > > > Regards & best wishes, > > Michael > > > > > > On Tue, 6 Apr 2004, Jose Duarte wrote: > > > > > Hi all > > > > > > I've got the file test.R with the following code: > > > > > > filenames <- c("1M2W050304.CEL", "2M2W050304.CEL", "3M2W050304.CEL", > > > "1M1W050304.CEL", "1M3W050304.CEL") > > > filepath <- "/net/array/WormDystrophy" > > > samples <- c("1M2W050304.CEL", "2M2W050304.CEL", "3M2W050304.CEL", > > > "1M1W050304.CEL", "1M3W050304.CEL") > > > custom <- c("rma", "quantiles", "pmonly", "medianpolish") > > > log2trans <- TRUE > > > library(affy) > > > library(gcrma) > > > library(vsn) > > > bgcorrect.methods <- c(bgcorrect.methods, "gcrma") > > > normalize.AffyBatch.methods <- c(normalize.AffyBatch.methods, "vsn") > > > express.summary.stat.methods <- c(express.summary.stat.methods, "rlm") > > > setwd(filepath) > > > exprset <- rma(ReadAffy(filenames = filenames)) > > > > > > > > > > > > I run it in batch mode from the linux command line with "R --no- save < > > > test.R". Everything is ok, except when executing the last line. The > > > rma() runs fine with the usual output: > > > > > > Background correcting > > > Normalizing > > > Calculating Expression > > > > > > But then it comes with the error: > > > > > > Error in rma(ReadAffy(filenames = filenames)) : > > > dimnames applied to non-array > > > Execution halted > > > > > > > > > > > > This is REALLY weird because: > > > > > > 1) It runs well in an interactive session just by copying and pasting > > > the code from the test.R file > > > > > > 2) It works fine if I change the order in which the file names are > > > given!! > > > > > > > > > Any ideas what the error means or what might be happening here? (I'm on > > > RedHat9, R 1.8.1, affy 1.3.28) > > > > > > Thanks > > > > > > Jose > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch > > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > > > > > >
ADD REPLY
0
Entering edit mode
What versions are you on? I hadn't had a look at this since my original posting back in April but having tried again now it seems that the problem is gone for me using R 1.9.0 and affy 1.4.30. Cheers Jose On Fri, 2004-06-18 at 12:42, Michael Seewald wrote: > It seems, I found the reason: > > When justGCRMA() is called in a subdirectory that contains the substring > "GMS_AllLCM-133A_Foo" it does NOT work. When I rename it to > "GMS_AllLCM-U133A_Foo" it runs fine. The "-" followed by a number is > apparently interpreted in a special (numerical?) way when justGCRMA reads the > CEL files from that directory. > > All of that applies only to the non-interactive session, it runs fine in the > interactive session. > > Best regards, > Michael > > > On Fri, 18 Jun 2004, Michael Seewald wrote: > > > > > Sorry, I have to correct myself. I just noted that the command fails *ONLY* in > > the non-interactive environemnt, e.g. when calling a script with "source". It > > works when I paste the command interactively into the R shell. This means it > > behaves exactly like Jose described.. > > > > Best wishes, > > Michael > > > > > > On Fri, 18 Jun 2004, Michael Seewald wrote: > > > > > > > > Dear Bioconductor people, dear Jean and Rafael, > > > > > > I see the same problem as Jose described (see below) with justGCRMA(). > > > > > > The following (while located in a directory with CEL files) does not work: > > > > > > > DATA.A.GCRMA<-justGCRMA(phenoData=pd) > > > Computing affinities..Done. > > > Adjusting for optical effect......................Done. > > > Adjusting for non-specific binding.....................Done. > > > Normalizing > > > Calculating Expression > > > Error in just.gcrma(filenames = filenames, phenoData = phenoData, description > > > = description, : > > > dimnames applied to non-array > > > > > > Splitting the task into two commands works: > > > > > > > DATA.A.GCRMA<-justGCRMA() > > > Computing affinities..Done. > > > Adjusting for optical effect......................Done. > > > Adjusting for non-specific binding.....................Done. > > > Normalizing > > > Calculating Expression > > > > phenoData(DATA.A.GCRMA) <- pd > > > > > > There seems to be a (non-critical) bug hidden in the code for the phenotypic > > > data. By the way, doing the same with justRMA in one step works fine. > > > > > > Do you need more information for debugging? > > > > > > Regards & best wishes, > > > Michael > > >
ADD REPLY

Login before adding your answer.

Traffic: 310 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6