Hi Henrik,
Thanks for your quick reply. Here are the files in the directory
GenomeWideSNP_6.chrXprobes
GenomeWideSNP_6.chrYprobes
GenomeWideSNP_6,Full.cdf
GenomeWideSNP_6,Full,monocell.CDF
GenomeWideSNP_6,Full,na24,HB20080214.ufl
GenomeWideSNP_6,Full,na24,HB20080214.ugp
GenomeWideSNP_6.specialSNPs
Starting a fresh R session with just aroma.affymetrix gave the same
error message :(
Mark
On 31 Oct, 17:34, "Henrik Bengtsson" <[EMAIL PROTECTED]> wrote:
> Hi Mark,
>
>
>
> On Fri, Oct 31, 2008 at 10:05 AM, Mark Dunning <[EMAIL PROTECTED]> wrote:
>
> > 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)
>
> Could you list the files that you have in
> annotationData/chipTypes/GenomeWideSNP_6/ here? It could be a
> filename hickup.
>
> Another thing is to try to start a fresh R session and only load
> aroma.affymetrix - I noticed your sessionInfo() and there might be a
> clash with other package, although I don't think so.
>
> /Henrik
>
>
>
> > 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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