[BioC] Reading .bpmap files for homemade tiling arrays

[Patrick Schorderet]

Hello everybody,

I am trying to normalize some ChIP-chip data using rMAT and to do so,  
you have to feed your .bpmap to the program (the file contains  
information relating to the design of the Affymetrix tiling arrays).  
Unfortunately, I get an error saying I am working with doubles instead  
of the wanted integer. I have not changed the .bpmap file at all and I  
can make no sense of it because have nothing to open it properly. I  
guess it might be due to the customized array we are using. The sizes  
might be different?

Thanks for the help,

Patrick




bpmapA<-"PRNFGMm2b520462F_rev.bpmap"
 > celA<-c("WT1.CEL","WT2.CEL", "Input_1.CEL", "Input_2.CEL")
 > ERA<-BPMAPCelParser(bpmapA, celA, seqName="chr2")
Reading Sequence Information from ./PRNFGMm2b520462F_rev.bpmap
Erreur dans .ReadBPMAPSeq(BPMAPFileName, seqToRead, readPM = TRUE,  
readMM = FALSE,  :
   INTEGER() can only be applied to a 'integer', not a 'double'
De plus : Messages d'avis :
1: In max(range) : aucun argument pour max ; -Inf est renvoyé
2: In min(range) : aucun argument trouvé pour min ; Inf est renvoyé

sessionInfo()
R version 2.11.0 (2010-04-22)
i386-apple-darwin9.8.0

locale:
[1] fr_CH.UTF-8/fr_CH.UTF-8/C/C/fr_CH.UTF-8/fr_CH.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] rMAT_2.4.0        affxparser_1.20.0 Biobase_2.8.0     IRanges_1.6.0

loaded via a namespace (and not attached):
[1] tools_2.11.0