[BioC] CNTools error message

[nathalie]

Hi,
I am analysing CGH data using DNAcopy to create segmented data and 
CNTools package to reduce the segments by genes.
No issue there.

#I created the segmentList object using segment function of DNAcopy
segmentList<-segment(smooth.CNA_order1.5,undo.splits="sdundo",undo.SD=1.5,verbose=1)
mySeglist1.5<-segmentList[["output"]]
#then I create a CNSeg object
require(CNTools)
cnseg1.5=CNSeg(mySeglist1.5)
# use a geneInfoMouse list I have created, this is the format: chrom    
start      end             geneid  genename
head(geneInfoMouse)
   chrom    start      end             geneid genename
1    14 53989971 53990250 ENSMUSG00000076824   X76971
2    14 53047603 53048549 ENSMUSG00000076758  Gm13987
3    14 53344974 53346592 ENSMUSG00000076829  Gm13955
4    14 53363924 53364514 ENSMUSG00000076767  Gm13956
5    14 53373042 53373519 ENSMUSG00000076768    Gm701
6    14 53389428 53390065 ENSMUSG00000076769  Gm13959
convertedData1.5G<-getRS(cnseg1.5, by ="gene", imput=FALSE, XY=TRUE, 
geneMap = geneinfo, what="mean")
#success!

#Then I want to reduce the segment using the probe ID and location from 
agilent (AgilentProbesMouse), I have created the same type of 
geneInfoMouse file using the same header:chrom    start      
end             geneid  genename
head(AgilentProbesMouse)
   chrom   start     end         geneid    genename
1     1 3002738 3002797 A_67_P04000012     Unknown
2     1 3017822 3017881 A_67_P04000019     Unknown
3     1 3027731 3027790 A_67_P04000027     Unknown
4     1 3036221 3036280 A_67_P04000032     Unknown
5     1 3053985 3054044 A_67_P04000058     Unknown
6     1 3063893 3063952 A_67_P04000065 gb|AK016604

#the only difference is this file is much bigger 468k lines vs 36k for 
the geneInfoMouse
#If I then use the same function as before on my segment pbject with the 
probe file
  convertedData1.5P<-getRS(cnseg1.5, by ="gene", imput=FALSE, XY=TRUE, 
geneMap = AgilentProbesMouse, what="mean")
#I got this error
Error in FUN(X[[1L]], ...) : NA/NaN/Inf in foreign function call (arg 2)

#If I reduce my geneInfoMouse to 36K lines, it works, Is there a size 
limit for this getRS function and can I change this?

I am sorry I can't  attaching any files as there are too large.
thanks for any advice, I guess I will start by\ spliting my probe file.
Nat
 > sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
  [5] LC_MONETARY=C              LC_MESSAGES=C
  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] CNTools_1.6.0     genefilter_1.30.0

loaded via a namespace (and not attached):
[1] annotate_1.26.1      AnnotationDbi_1.10.1 Biobase_2.8.0
[4] DBI_0.2-5            RSQLite_0.9-1        splines_2.13.0
[7] survival_2.35-8      xtable_1.6-0
reduced_bygene1.5=rs(convertedData1.5G)
  write.table(reduced_bygene1.5, file="reduced_bygene1.5.xls", sep="\t", 
row.names=F)




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