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:
 [1] hgu133plus2probe_2.2.0 hgu133plus2cdf_2.2.0   hgu133plus2.db_2.2.0
 [4] hgu133plus2_2.2.0      hgu133aprobe_2.2.0     hgu133acdf_2.2.0
 [7] hgu133a_2.2.0          hgu133a.db_2.2.0       AnnotationDbi_1.2.1
[10] RSQLite_0.6-8          DBI_0.2-4              matchprobes_1.12.0
[13] RColorBrewer_1.0-2     affy_1.18.1            preprocessCore_1.2.0
[16] affyio_1.8.0           Biobase_2.0.1          limma_2.14.2

I have reproduce my code on 3 differents Unix machines
the used classic code (is fonctionnal) :

targets_Berthiaume = readTargets("Berthiaume_CEL/target_CUFI_NULI.txt", sep="" )
 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
 
VOISIN Greg. 
Etudiant au Doctorat en Bioinformatique 
Université de Montreal
Centre de recherche du CHUM. 
Institut de Recherche en Immunologie et Cancérologie



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