Hi Guido,
thanks a bunch for this.
I've made a patch available until next release of aroma.affymetrix.
Just do the following (only once) to install the patches:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
FYI, I did use the 'pdName' variable (which is defined later in the
code) and not the 'pdpkg', because that is what the original author(s)
used to generate the CDF filename.
/Henrik
On Fri, Dec 3, 2010 at 1:07 PM, Hooiveld, Guido <guido.hooiv...@wur.nl> wrote:
> 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
> email: guido.hooiv...@wur.nl
>
>
> --
> 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
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>
--
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
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