[BioC] Problem with justSNPRMA, library "oligo"

alessio boattini alessio.boattini2 at unibo.it
Tue Feb 10 14:58:11 CET 2009


Dear All,

I am working with Affymetrix Genome Wide Human SNP Array 6.0 data.
While pre-processing the data with the justSNPRMA function (library
"oligo"), I obtained the error described below. 
An analogous problem was reported there: 
http://article.gmane.org/gmane.science.biology.informatics.conductor/17495
but there was no answer.
Any hint?
Many thanks
Alessio

> library(oligo)
...
> setwd("/home/alessio/Documents/martinelli")
> fullFilenames=list.celfiles()
> fullFilenames
[1] "20081009_1_SNP6.CEL"
> preProcData=justSNPRMA(fullFilenames)
Reading CEL files.
Normalizing to Hapmap.
Summarizing.
Error in justSNPRMA(fullFilenames) : 
  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(fullFilenames)

> sessionInfo()
R version 2.8.1 (2008-12-22) 
i686-pc-linux-gnu 

locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
 [1] pd.genomewidesnp.6_0.4.2 oligo_1.6.0
oligoClasses_1.4.0      
 [4] affxparser_1.14.2        AnnotationDbi_1.4.2
preprocessCore_1.4.0    
 [7] RSQLite_0.7-1            DBI_0.2-4
Biobase_2.2.1           
[10] vegan_1.15-1



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