[BioC] Parsing Illumina Golden Gate idat files

[Mike Walter]

Dear List,

I have a series of golden gate cancer panel SNP data and wanted to use the beadarraySNP package to analyse the data. Unfortunately, I only have the idat files and not the csv files. Thus I tried 'crlmm' package to parse the idats for the red and green channel to create the csv tables. I get some error message which is most likely related to the format of the files.

library(ff)
library(crlmm)

f.GG = list.files()

x = crlmm:::readIDAT(f.GG)
Error in matrix(0, nFields, 3) : too many elements specified


x = crlmm:::readIdatFiles(path=getwd()) #I know that this is for Infinium data, I tried anyway
reading 4075501002_R001_C001    _Grn.idat      Error in matrix(0, nFields, 3) : too many elements specified

Does someone has an idea how to read in the files? Any hint is welcome.

Thanks and kind regards,

Mike


> sessionInfo()
R version 2.11.1 (2010-05-31) 
i386-pc-mingw32 

locale:
[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252   
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.1252    

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

other attached packages:
[1] crlmm_1.6.5         oligoClasses_1.10.0 Biobase_2.8.0      
[4] ff_2.1-2            bit_1.1-4          

loaded via a namespace (and not attached):
 [1] affyio_1.16.0         annotate_1.26.1       AnnotationDbi_1.10.2 
 [4] Biostrings_2.16.9     DBI_0.2-5             ellipse_0.3-5        
 [7] genefilter_1.30.0     IRanges_1.6.16        mvtnorm_0.9-92       
[10] preprocessCore_1.10.0 RSQLite_0.9-2         splines_2.11.1       
[13] survival_2.35-8       xtable_1.5-6