[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]

Patrick Aboyoun paboyoun at fhcrc.org
Fri Oct 31 20:29:21 CET 2008


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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