RE: [aroma.affymetrix] Construct cdf file from pgf, clf and gene mapping file
Hi, I was a little curious to know what these scripts are able to construct/convert, so I had a quick look at the codes. @ Elizabeth (or others): Although I am not planning to use these (yet), there is one thing that (naively?) did not become immediately clear to me: what is the expected content of the file annotExonBoundaries that is required for the (1st) function annotateProbesets.R, (and how would generate such file)? From the description in the script: exonBoundariesFile=file name of deliminated file with the exon boundaries that you want to map the probesets to. ##annotExonBoundaries-file.path(outdir,exonBoundaries_proteinCoding_20080819.txt) Thanks, Guido - 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 email: guido.hooiv...@wur.nl internet: http://nutrigene.4t.com http://scholar.google.com/citations?user=qFHaMnoJ http://www.researcherid.com/rid/F-4912-2010 -Original Message- From: aroma-affymetrix@googlegroups.com [mailto:aroma-affymetrix@googlegroups.com] On Behalf Of Henrik Bengtsson Sent: Wednesday, January 22, 2014 21:15 To: aroma-affymetrix@googlegroups.com Subject: Re: [aroma.affymetrix] Construct cdf file from pgf, clf and gene mapping file Alright, so Elizabeth Purdom found the missing files and kindly sent them to me. I've now uploaded them the http://aroma-project.org server and updated the links on http://aroma-project.org/node/40 accordingly. Hope this helps Henrik On Tue, Jan 21, 2014 at 3:35 PM, Henrik Bengtsson henrik.bengts...@aroma-project.org wrote: Hi, thanks for reporting on this. On Mon, Jan 20, 2014 at 2:09 PM, Guilherme Rocha gvro...@gmail.com wrote: Dear all, Does anybody know of any good tools for constructing a cdf file from affy pgf and clf files? It appears that such tools exist: http://www.aroma-project.org/node/40 The problem is the following 3 links in above address are broken: 1)http://bcgc.lbl.gov/cdfFiles/flat2Cdf.R Flat2cdf.R (constructs a cdf file from a flat file) It turns out that that file is the same as http://bioinf.wehi.edu.au/folders/mrobinson/exon/flat2Cdf.R I've update the webpage to link to that instead (for now). 2)http://bcgc.lbl.gov/cdfFiles/combineProbeInfo.pl combineProbeInfo.pl (combines pgf and clf files into single flat file with each row containing most of the information needed for each probe) Unfortunately, I cannot locate this elsewhere. 3)http://bcgc.lbl.gov/cdfFiles/addGeneId.pl addGeneId.pl (takes output of previous pl script and merge it with probeset-gene map to generate flat file needed by flat2cdf) Unfortunately, same for this one (and the other links on that page). If you can generate a flat text-files as on illustrated on that page, you could still create a CDF. However, note that the flat2Cdf() function is rather specific to gene-exon chip types, so if you're looking to create other types of CDF files, it won't work (at least not out of the box). I've updated http://aroma-project.org/node/40 with the following note: Note: Several of the links to the external third party R and Perl scripts are broken, i.e. annotateProbesets.R, convertProbesetCSV_differentInput.pl, selectProbes.pl combineProbeInfo.pl, addGeneId.pl. If you have any of these files sitting around, please consider sending them to use. Thanks /HB 2014-01-20 Thanks, Henrik Any help greatly appreciated. Thanks, Guilherme Rocha -- -- 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/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out. -- -- 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
Re: [aroma.affymetrix] Construct cdf file from pgf, clf and gene mapping file
Hi, thanks for reporting on this. On Mon, Jan 20, 2014 at 2:09 PM, Guilherme Rocha gvro...@gmail.com wrote: Dear all, Does anybody know of any good tools for constructing a cdf file from affy pgf and clf files? It appears that such tools exist: http://www.aroma-project.org/node/40 The problem is the following 3 links in above address are broken: 1)http://bcgc.lbl.gov/cdfFiles/flat2Cdf.R Flat2cdf.R (constructs a cdf file from a flat file) It turns out that that file is the same as http://bioinf.wehi.edu.au/folders/mrobinson/exon/flat2Cdf.R I've update the webpage to link to that instead (for now). 2)http://bcgc.lbl.gov/cdfFiles/combineProbeInfo.pl combineProbeInfo.pl (combines pgf and clf files into single flat file with each row containing most of the information needed for each probe) Unfortunately, I cannot locate this elsewhere. 3)http://bcgc.lbl.gov/cdfFiles/addGeneId.pl addGeneId.pl (takes output of previous pl script and merge it with probeset-gene map to generate flat file needed by flat2cdf) Unfortunately, same for this one (and the other links on that page). If you can generate a flat text-files as on illustrated on that page, you could still create a CDF. However, note that the flat2Cdf() function is rather specific to gene-exon chip types, so if you're looking to create other types of CDF files, it won't work (at least not out of the box). I've updated http://aroma-project.org/node/40 with the following note: Note: Several of the links to the external third party R and Perl scripts are broken, i.e. annotateProbesets.R, convertProbesetCSV_differentInput.pl, selectProbes.pl combineProbeInfo.pl, addGeneId.pl. If you have any of these files sitting around, please consider sending them to use. Thanks /HB 2014-01-20 Thanks, Henrik Any help greatly appreciated. Thanks, Guilherme Rocha -- -- 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/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out. -- -- 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/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
[aroma.affymetrix] Construct cdf file from pgf, clf and gene mapping file
Dear all, Does anybody know of any good tools for constructing a cdf file from affy pgf and clf files? It appears that such tools exist: http://www.aroma-project.org/node/40 The problem is the following 3 links in above address are broken: 1)http://bcgc.lbl.gov/cdfFiles/flat2Cdf.R Flat2cdf.R (constructs a cdf file from a flat file) 2)http://bcgc.lbl.gov/cdfFiles/combineProbeInfo.pl combineProbeInfo.pl (combines pgf and clf files into single flat file with each row containing most of the information needed for each probe) 3)http://bcgc.lbl.gov/cdfFiles/addGeneId.pl addGeneId.pl (takes output of previous pl script and merge it with probeset-gene map to generate flat file needed by flat2cdf) Any help greatly appreciated. Thanks, Guilherme Rocha -- -- 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/ --- You received this message because you are subscribed to the Google Groups aroma.affymetrix group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
