Dear Henrik,
I would like to report a problem with the function pdInfo2Cdf.R
I know this function is not part of the core functionality of aroma.affymetrix,
but i thought it still would be good to inform you about the error i found.
Meanwhile I found out it is caused by line 71:
the argument 'pdName' should actually be 'pdpkg' in
line 71 - filename <- sprintf("%s.cdf", pdName);
If I apply the above-mentioned modification, source the modified function
'pdInfo2Cdf_MOD.R, and then run the function everything goes fine (see below).
For your convenience I have uploaded a CEL file required to execute the
function (for testing purposes):
https://sendit.wur.nl/Download.aspx?id=e0c9eea2-5f72-454c-873d-f1a215f57d1c
Note: link is alive for 5 days, and/or allows max 20 downloads.
Regards,
Guido
> library(aroma.affymetrix)
<<SNIP>>
> pdInfo2Cdf("pd.mogene.1.1.st.v1", "MouseBrain_1.CEL");
<<SNIP>>
PdInfo2Cdf()...
Error in sprintf("%s.cdf", pdName) : object 'pdName' not found
In addition: Warning message:
In fcn(...) : Packages reordered in search path: package:oligo
> source("pdInfo2Cdf_MOD.R")
> pdInfo2Cdf("pd.mogene.1.1.st.v1", "MouseBrain_1.CEL");
PdInfo2Cdf()...
Loading required package: pd.mogene.1.1.st.v1
Reading auxillary CEL file...
Platform design info loaded.
Reading in : MouseBrain_1.CEL
Reading auxillary CEL file...done
Querying Platform Design database...
Querying Platform Design database...done
Creating list from query table...
Creating list from query table...done
Creating CDF list structure...
Creating CDF list for 241576 units
Creating CDF list structure...done
Writing CDF file...
Writing CDF file...
Pathname: pd.mogene.1.1.st.v1.cdf
Writes CDF header and unit names...
Writes CDF header and unit names...done
Writes QC units...
Writes QC units...done
Writes 241576 units...
Writes 241576 units...done
Writing CDF file...done
Writing CDF file...done
PdInfo2Cdf()...done
>
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] pdInfoBuilder_1.14.1 oligoClasses_1.12.1 RSQLite_0.9-4
[4] DBI_0.2-5 Biobase_2.10.0 aroma.affymetrix_1.8.0
[7] aroma.apd_0.1.7 affxparser_1.22.0 R.huge_0.2.0
[10] aroma.core_1.8.0 aroma.light_1.18.2 matrixStats_0.2.2
[13] R.rsp_0.4.0 R.cache_0.3.0 R.filesets_0.9.1
[16] digest_0.4.2 R.utils_1.5.8 R.oo_1.7.4
[19] oligo_1.14.0 R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] affyio_1.19.2 Biostrings_2.18.0 IRanges_1.8.3
[4] preprocessCore_1.12.0 splines_2.12.0
------------------------------------------------
Guido Hooiveld, PhD
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
Wageningen University
Biotechnion, Bomenweg 2
NL-6703 HD Wageningen
the Netherlands
tel: (+)31 317 485788
fax: (+)31 317 483342
internet: http://nutrigene.4t.com<http://nutrigene.4t.com/>
email: guido.hooiv...@wur.nl
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