[BioC] combineaffybatch and Subsscript out of bound

[Wolfgang Huber]

Dear Greg

it seems difficult to do much about your problem without being able to 
reproduce it.  Would it be possible for you to reproduce your problem 
with just *two* CEL files (one of each type),  and then making these (or 
better even, the corresponding AffyBatches saved using "save"), as well 
as your script, available to this list?

Also, if you are adventurous, you could use the debugger with

  options(error=recover)

and explore the local variables and code in the combineAffyBatch 
function where the error occurs.

Thanks and best wishes
	Wolfgang.

gregory voisin wrote:
> Hi , 
> I try to use combineAffyBatch in my experiment:
> 
> 2experiment using Hgu133a (10 versus 10) et hg1332plus( 3 versus 3),
> R version 2.7.0 (2008-04-22)
> x86_64-unknown-linux-gnu
> 8 gig RAM
> other attached packages:
> Â [1] hgu133plus2probe_2.2.0 hgu133plus2cdf_2.2.0Â Â  hgu133plus2.db_2.2.0
> Â [4] hgu133plus2_2.2.0Â Â Â Â Â  hgu133aprobe_2.2.0Â Â Â Â  hgu133acdf_2.2.0
> Â [7] hgu133a_2.2.0Â Â Â Â Â Â Â Â Â  hgu133a.db_2.2.0Â Â Â Â Â Â  AnnotationDbi_1.2.1
> [10] RSQLite_0.6-8Â Â Â Â Â Â Â Â Â  DBI_0.2-4Â Â Â Â Â Â Â Â Â Â Â Â Â  matchprobes_1.12.0
> [13] RColorBrewer_1.0-2Â Â Â Â  affy_1.18.1Â Â Â Â Â Â Â Â Â Â Â  preprocessCore_1.2.0
> [16] affyio_1.8.0Â Â Â Â Â Â Â Â Â Â  Biobase_2.0.1Â Â Â Â Â Â Â Â Â  limma_2.14.2
> 
> I have reproduce my code on 3 differents Unix machines
> the used classic code (is fonctionnal)Â :
> 
> targets_Berthiaume = readTargets("Berthiaume_CEL/target_CUFI_NULI.txt", sep="" )
> Â abatch_Berthiaume = ReadAffy(filenames = targets_Berthiaume$FileName, celfile.path= "Berthiaume_CEL")
> targets_Zabner = readTargets("Zabner_CEL/target_CF_NCF.txt", sep="")
> abatch_Zabner = ReadAffy(filenames = targets_Zabner$FileName, celfile.path= "Zabner_CEL")
> ##################################################################
>  abatch_combin <- combineAffyBatch(list(abatch_Berthiaume, abatch_Zabner), c("h gu133aprobe", "hgu133plus2probe"), newcdf="hgu133combin", verbose=TRUE)
> 
> package:hgu133aprobe    hgu133aprobe
> ackage:hgu133plus2probe        hgu133plus2probe
> 241837 unique probes in common
> Error: subscript out of bounds
> I appreciate your help to interprete this message (I Imagine that is linked to the length of data), and to solve it 
> Thanks
> Â 
> VOISIN Greg. 
> Etudiant au Doctorat en Bioinformatique 
> Université de Montreal
> Centre de recherche du CHUM. 
> Institut de Recherche en Immunologie et Cancérologie
> 
> 
> 
>       _____________________________________________________________________________ 
> 
> o.fr
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> 
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