[BioC] Problems with oligo and pd.genomewidesnp.6

[Jeremy Silver]

Hello,

I'm trying to call genotypes from Affymetrix SNP 6.0 chips using the 
oligo package. I've run into a small problem, that I think may be due to 
the differences between the bioconductor package pd.genomewidesnp.6 and 
the other pd.*.* annotation packages. Details are below. Any ideas?

Thanks,

Jeremy

###############################################

# here are the names of the .CEL files

 > fullFilenamesOrigCelFiles[1:5]
[1] "rawData/tds2008/GenomeWideSNP_6/SNP001_01_M001A.CEL"
[2] "rawData/tds2008/GenomeWideSNP_6/SNP001_02_M003A.CEL"
[3] "rawData/tds2008/GenomeWideSNP_6/SNP001_03_M007A.CEL"
[4] "rawData/tds2008/GenomeWideSNP_6/SNP001_04_M015A.CEL"
[5] "rawData/tds2008/GenomeWideSNP_6/SNP001_06_M026A.CEL"

# call justSNPRMA

 > snpRmaResults <- justSNPRMA(filenames = fullFilenamesOrigCelFiles[1:5],
+                             verbose = TRUE,
+                             phenoData = NULL,
+                             normalizeToHapmap = TRUE)
Reading CEL files.
Normalizing to Hapmap.
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file '', probable reason 'No such file or 
directory'
 > traceback()
3: readChar(con, 5L, useBytes = TRUE)
2: load(system.file("extdata", paste(pkgname, "Ref.rda", sep = ""),
       package = pkgname))
1: justSNPRMA(filenames = fullFilenamesOrigCelFiles[1:5], verbose = TRUE,
       phenoData = NULL, normalizeToHapmap = TRUE)
 > sessionInfo()
R version 2.7.0 (2008-04-22)
i686-pc-linux-gnu

locale:
C

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

other attached packages:
 [1] pd.genomewidesnp.6_0.4.1 aroma.affymetrix_0.9.1   
aroma.apd_0.1.3        
 [4] R.huge_0.1.5             digest_0.3.1             
aroma.light_1.7.2      
 [7] R.rsp_0.3.4              R.cache_0.1.7            
R.utils_1.0.2          
[10] R.oo_1.4.3               R.methodsS3_1.0.1        
oligo_1.4.0            
[13] oligoClasses_1.2.0       affxparser_1.11.14       
AnnotationDbi_1.2.1    
[16] preprocessCore_1.1.9     RSQLite_0.6-8            
DBI_0.2-4              
[19] Biobase_1.99.10        

# See if we can find the problem - the following three lines come from 
justSNPRMA

 > filenames <- fullFilenamesOrigCelFiles[1:5]
 >     headdetails <- readCelHeader(filenames[1])
 >    pkgname <- cleanPlatformName(headdetails[["chiptype"]])

# The problematic line asks to load the following file....

 > system.file("extdata", paste(pkgname, "Ref.rda", sep = ""), package = 
pkgname)
[1] ""

# ... which doesn't seem to exist. Here's the folder we're looking at

 > system.file("extdata", package = pkgname)
[1] "$HOME/R/i686-pc-linux-gnu-library/2.7/pd.genomewidesnp.6/extdata"

# ... and here are the files it contains

 > list.files(system.file("extdata", package = pkgname))
[1] "pd.genomewidesnp.6.sqlite" "seqMat.rda"              

Looks like we were trying to load a file called 
"pd.genomewidesnp.6Ref.rda" from this folder.