[BioC] Nimblegen CGH ringo to snapCGH

[Chris Fenton]

Has anyone gotten nimblegen CGH data from Ringo into snapCGH. 

I have looked at
https://stat.ethz.ch/pipermail/bioconductor/2006-October/014724.html

but it seems that Nimblegen has yet again changed format. For instance I
find no file remotely named ORDER_ID3051_SampleKey.txt. I do have a file
sample_key.txt 
"""
ARRAY_ID        CY3_SAMPLE_NAME CY5_SAMPLE_NAME
39450A01_290310 patient_f       male_ref
""" 

but I doubt looking at the code this is the right file. 
I tried a small hack with little luck below. 

Any help greatly appreciated. 

Chris 

""""

library('Ringo') 
library('snapCGH') 
exRG     <- readNimblegen('samples.txt', 'spots.txt')
ma       <- preprocess(exRG, method='nimblegen', returnMAList=TRUE) 
ma$design <- c(-1, -1) 

# remove non chromosomal probes 
probes   <- grep('CHR', ma$genes[,'ID']) 
ma$genes <- ma$genes[probes,]
ma$M     <- ma$M[probes,]
ma$A     <- ma$A[probes,]


#parse chromosomes from gene name 
Chr        <- gsub('CHR','', ma$genes[,'ID']) 
Chr        <- gsub('FS.*','', Chr) 

# stolen from read.clonesinfor 
indX       <- which(Chr == "X" | Chr == "x")
indY       <- which(Chr == "Y" | Chr == "y")
Chr[indX]  <- 23
Chr[indY]  <- 24
rg1 <- RG.MA(ma) 
rg1$genes <- data.frame(rg1$genes, 'Position'=rg1$genes[, 'POSITION'],
'Chr'=as.numeric(Chr)) 

ma2 <- processCGH(rg1) 

""""

I get 

Error: subscript out of bounds

on the processCGH. 


sessionInfo()
R version 2.10.1 (2009-12-14) 
i686-pc-linux-gnu 

locale:
[1] C

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

other attached packages:
 [1] snapCGH_1.16.0     aCGH_1.22.0        multtest_2.2.0
survival_2.35-7   
 [5] cluster_1.12.1     GLAD_2.6.0         DNAcopy_1.20.0
tilingArray_1.24.0
 [9] pixmap_0.4-10      Ringo_1.10.0       Matrix_0.999375-33
lattice_0.17-26   
[13] limma_3.2.1        RColorBrewer_1.0-2 Biobase_2.6.1     

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.8.1  DBI_0.2-5            MASS_7.3-4          
 [4] RSQLite_0.8-2        affy_1.24.2          affyio_1.14.0       
 [7] annotate_1.24.1      genefilter_1.28.2    preprocessCore_1.8.0
[10] strucchange_1.4-0    tools_2.10.1         vsn_3.14.0          
[13] xtable_1.5-6