Hello all,
Just started using aroma, and I'm afraid I'm not getting very far :( I
think I've got a handle on how the directory structure works and can
read in some information from the cdf file correctly, but
getGenomeInformation is giving an error.
What is quite strange is that a colleague is able to execute the
command correctly from the same directory, although they are running a
slightly older version of aroma.affymetrix.
> cdf <- AffymetrixCdfFile$fromChipType("GenomeWideSNP_6", tags="Full")
> cdf
AffymetrixCdfFile:
Path: annotationData/chipTypes/GenomeWideSNP_6
Filename: GenomeWideSNP_6,Full.cdf
Filesize: 470.44MB
Chip type: GenomeWideSNP_6,Full
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 1881415
Cells per unit: 3.66
Number of QC units: 4
> si <- getSnpInformation(cdf)
> print(si)
UflSnpInformation:
Name: GenomeWideSNP_6
Tags: Full,na24,HB20080214
Pathname: annotationData/chipTypes/GenomeWideSNP_6/
GenomeWideSNP_6,Full,na24,HB20080214.ufl
File size: 7.18MB
RAM: 0.00MB
Chip type: GenomeWideSNP_6,Full
Number of enzymes: 2
> gi <- getGenomeInformation(cdf)
Error in list("getGenomeInformation(cdf)" = <environment>,
"getGenomeInformation.AffymetrixCdfFile(cdf)" = <environment>, :
[2008-10-31 16:49:35] Exception: Failed to retrieve genome information
for this chip type: GenomeWideSNP_6
at throw(Exception(...))
at throw.default("Failed to retrieve genome information for this
chip type: ",
at throw("Failed to retrieve genome information for this chip type:
", chipTyp
at getGenomeInformation.AffymetrixCdfFile(cdf)
at getGenomeInformation(cdf)
Thanks in advance for any help,
Cheers,
Mark
> sessionInfo()
R version 2.7.0 (2008-04-22)
x86_64-unknown-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] tools splines stats graphics grDevices utils
datasets
[8] methods base
other attached packages:
[1] geneplotter_1.18.0 annotate_1.18.0
xtable_1.5-2
[4] AnnotationDbi_1.2.1 RSQLite_0.6-8
DBI_0.2-4
[7] lattice_0.17-6 DNAcopy_1.14.0
aCGH_1.14.0
[10] sma_0.5.15 multtest_1.20.0
Biobase_2.0.1
[13] survival_2.34-1 cluster_1.11.10
aroma.affymetrix_0.9.5
[16] aroma.apd_0.1.3 R.huge_0.1.6
affxparser_1.14.0
[19] aroma.core_0.9.5 aroma.light_1.9.2
digest_0.3.1
[22] matrixStats_0.1.3 R.rsp_0.3.4
R.cache_0.1.7
[25] R.utils_1.0.9 R.oo_1.4.5
R.methodsS3_1.0.3
loaded via a namespace (and not attached):
[1] grid_2.7.0 KernSmooth_2.22-22 RColorBrewer_1.0-2
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