Dear Henrik,
I am trying to analyse some Affy6 data, but I am stuck at reading the
ugp file.
For some reasons, I got "Exception: Failed to retrieve genome
information for this chip type: GenomeWideSNP_6"
(cf code and sessionInfo below).
The files under annotationData/chipTypes/GenomeWideSNP_6 are :
GenomeWideSNP_6,Full.cdf (downloaded today from the Affy website)
GenomeWideSNP_6,Full,HB20080710.acs
GenomeWideSNP_6,Full,na26,HB20080821.ugp
GenomeWideSNP_6,na26,HB20080821.ufl
Are there any newer annotation files I need to download or am I simply
doing something wrong?
Many thanks,
Armand
> library("aroma.affymetrix")
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.0.3 (2008-07-02) successfully loaded. See ?R.methodsS3
for help.
R.oo v1.4.6 (2008-08-11) successfully loaded. See ?R.oo for help.
R.utils v1.1.3 (2009-01-12) successfully loaded. See ?R.utils for help.
Loading required package: aroma.core
Loading required package: R.cache
R.cache v0.1.7 (2008-02-27) successfully loaded. See ?R.cache for help.
Loading required package: R.rsp
R.rsp v0.3.4 (2008-03-06) successfully loaded. See ?R.rsp for help.
Type browseRsp() to open the RSP main menu in your browser.
Loading required package: matrixStats
Loading required package: digest
Loading required package: aroma.light
aroma.light v1.11.1 (2009-01-12) successfully loaded. See ?aroma.light
for help.
aroma.core v1.0.0 (2009-01-12) successfully loaded. See ?aroma.core for
help.
Loading required package: affxparser
Loading required package: R.huge
R.huge v0.1.6 (2008-07-03) successfully loaded. See ?R.huge for help.
Loading required package: aroma.apd
aroma.apd v0.1.3 (2006-06-14) successfully loaded. See ?aroma.apd for help.
aroma.affymetrix v1.0.0 (2009-01-12) successfully loaded. See
?aroma.affymetrix for help.
>
> log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE)
> options(digits=4)
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full")
> print(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
> gi <- getGenomeInformation(cdf)
Error in list("getGenomeInformation(cdf)" = <environment>,
"getGenomeInformation.AffymetrixCdfFile(cdf)" = <environment>, :
[2009-02-10 19:18:09] 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)
> sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] aroma.affymetrix_1.0.0 aroma.apd_0.1.3 R.huge_0.1.6
[4] affxparser_1.14.0 aroma.core_1.0.0 aroma.light_1.11.1
[7] digest_0.3.1 matrixStats_0.1.3 R.rsp_0.3.4
[10] R.cache_0.1.7 R.utils_1.1.3 R.oo_1.4.6
[13] R.methodsS3_1.0.3
--~--~---------~--~----~------------~-------~--~----~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group.
To post to this group, send email to [email protected]
To unsubscribe from this group, send email to
[email protected]
For more options, visit this group at
http://groups.google.com/group/aroma-affymetrix?hl=en
-~----------~----~----~----~------~----~------~--~---
