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.
