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 > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > -- 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 with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/