[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]

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
>>
>> _______________________________________________
>> 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
>