Entering edit mode
Jeremy Silver
▴
10
@jeremy-silver-2813
Last seen 10.3 years ago
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.
