Hello All,
I use pd.genomewidesnp.6 library with oligo and at summarization phase I
obtain the following error:
What can be the problem?
Many thanks for your advices!
Best,
Sergii
 
file= "F02_MDA-MB-175-VII_221007.CEL"
preProcessedData <- justSNPRMA(file)
 
Reading CEL files.
Normalizing to Hapmap.
Summarizing.
Error in justSNPRMA(file) : 
INTEGER() can only be applied to a 'integer', not a 'NULL'
 
 traceback()
2: .Call("rma_c_complete_copy", tmpExprs, tmpExprs, pnVec,
length(unique(pnVec)), 
       body(bg.dens), new.env(), FALSE, FALSE, as.integer(2), PACKAGE =
"oligo")
1: justSNPRMA(file)

sessionInfo()
R version 2.6.1 (2007-11-26) 
i386-pc-mingw32 
 
locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_MONETARY=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252
 
attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     datasets

[8] methods   base     
 
other attached packages:
[1] pd.genomewidesnp.6_0.3.5 oligo_1.3.13
oligoClasses_1.1.11     
[4] affxparser_1.10.2        AnnotationDbi_1.0.6
preprocessCore_1.0.0    
[7] RSQLite_0.5-6            DBI_0.2-4                Biobase_1.16.2

 
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17


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