[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]

[Wolfgang Huber]

Dear Charlie,

I agree a lot with you that this is troublesome... but I would be
interested in discussing

(i) do you (and others) consider this an "error", or rather "bad
behaviour" or "poor performance"?

(ii) and is it gcrma, or LPE that errs or poorly performs?

(iii) and are any of the maintainers of these packages interested in
these questions?

Best wishes
 Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber


31/10/2008 20:05 charliew scripsit
> 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
>>>