[BioC] LPE error caused by gcRMA [Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]), mean(var.M.adap[i + : replacement has length zero]
charliew
charliew at MIT.EDU
Fri Oct 31 21:05:37 CET 2008
Hi Patrick,
Thanks a lot for the quick reply. I updated the package and it
didn't fix the error.
c
On Oct 31, 2008, at 3:29 PM, Patrick Aboyoun wrote:
> Charlie,
> I don't know if this is related to you issue, but a bug in the gcrma
> package was just fixed and there is a version 2.14.1 is now up on
> bioconductor.org. Update to the latest version of gcrma and see if
> it addresses your issue.
>
>
> Patrick
>
>
>
> charliew wrote:
>> Dear List,
>> I've encountered the following error when running LPE:
>>
>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]),
>> mean(var.M.adap[i + :
>> replacement has length zero
>>
>> It happens when the CEL files have been processed with gcRMA but
>> not when they have been processed with RMA.
>> I'm not positive about this but I think this error first started
>> happening with the upgrade to gcRMA 2.x
>> I think it is happening because gcRMA is producing a lot of probes
>> with identical expression values.
>>
>> Here is a test session that causes the error. Upon request I can
>> provide a tarball of the test data but any collection of CEL files
>> will reproduce the error.
>> The error also occurs if you run gcRMA from within onecolorGUI or
>> affylmGUI.
>> It also happens if you first write the expression data to a file
>> with write.exprs, then read it back in with read.table.
>>
>> #Loading the packages
>> > library(affy)
>> Loading required package: Biobase
>> Loading required package: tools
>>
>> > library(gcrma)
>> Loading required package: matchprobes
>> Loading required package: splines
>>
>> > library(LPE)
>> > set.seed(0)
>>
>> #Reading in 4 CEL files
>> > test.Dat<-ReadAffy()
>>
>> #Summarizing with gcRMA
>> > test.gcrma<-gcrma(test.Dat)
>> Adjusting for non-specific binding....Done.
>> Normalizing
>> Calculating Expression
>>
>> #Summarizing with RMA
>> > test.rma<-rma(test.Dat)
>> Background correcting
>> Normalizing
>> Calculating Expression
>>
>> #Extracting gcRMA assay data
>> > test.gcrma.MAT<-exprs(test.gcrma)
>> > dim(test.gcrma.MAT)
>> [1] 15611 4
>>
>> #Extracting RMA assay data
>>
>> > test.rma.MAT<-exprs(test.rma)
>> > dim(test.rma.MAT)
>> [1] 15611 4
>>
>> #Running LPE function on gcRMA data and the resulting error
>> > var.test.gcrma<-baseOlig.error(test.gcrma.MAT, q= 0.01)
>> Error in var.M.adap[i] <- ifelse(!is.na(var.M.adap[i - 1]),
>> mean(var.M.adap[i + :
>> replacement has length zero
>>
>> #Running LPE function on RMA data - it successfully completes
>> > var.test.rma<-baseOlig.error(test.rma.MAT, q= 0.01)
>> >
>>
>> #My session info
>> > sessionInfo()
>> R version 2.8.0 (2008-10-20)
>> i386-apple-darwin8.11.1
>>
>> locale:
>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] splines tools stats graphics grDevices utils
>> datasets methods base
>>
>> other attached packages:
>> [1] xenopuslaevisprobe_2.3.0 xenopuslaeviscdf_2.3.0
>> LPE_1.16.0 gcrma_2.14.0
>> matchprobes_1.14.0 affy_1.20.0 Biobase_2.2.0
>>
>> loaded via a namespace (and not attached):
>> [1] affyio_1.10.0 preprocessCore_1.4.0
>>
>> Thanks a lot for your help
>>
>> Charlie
>>
>> ----------------------------------------------------------------------------
>> Charlie Whittaker, Ph.D.
>> Bioinformatics and Computing Core Facility
>> The David H. Koch Institute for Integrative Cancer Research At MIT
>> 77 Mass Ave E18-366
>> Cambridge, MA 02139
>>
>> 617-324-0337
>>
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