Hi all, This is to inform you that (finally) we have put on-line the binary CDFs for 18 arrays. Please find them on our server (Table 4): http://nmg-r.bioinformatics.nl/NuGO_R.html
CDFs are available for these arrays: AraGene-1_0-st AraGene-1_1-st HuGene-1_0-st-v1 HuGene-1_1-st-v1 HuGene-2_0-st HuGene-2_1-st MoGene-1_0-st-v1 MoGene-1_1-st-v1 MoGene-2_0-st MoGene-2_1-st PorGene-1_0-st PorGene-1_1-st RaGene-1_0-st-v1 RaGene-1_1-st-v1 RaGene-2_0-st RaGene-2_1-st ZebGene-1_0-st ZebGene-1_1-st >From the readme.txt: - This binary CDF has been created from a platform design info (PdInfo) package available in R version 2.15.2/ Bioconductor version 2.11 using functions available the library aroma.affymetrix v2.8.0. - 'Probesets' are based on transcript clusters (meta-probeset) as defined by Affymetrix in the MPS (meta probeset) file, as is also reflected in the filename. - A transcript cluster is a group of one or more probes covering a region of the genome reflecting all the exonic transcription evidence known for the region and corresponding to a known or putative gene. The underlying exonic evidence can come from transcripts of well-annotated genes or predicted genes. A given transcript cluster may have a variety of assigned RNAs, classified according to the NetAffx transcript classification system. - Please note that these are unofficial CDFs (i.e. CDF files not supported or endorsed by Affymetrix), so you agree to use them at your own risk! However, whenever possible*, binary CDFs have been confirmed to be working with aroma.affymetrix. - In principle the binary CDFs could also be used with stand-alone applications such as dChip. Unfortunately, at the moment of writing, dChip is not able to load these files. The author of dChip has been informed about this, but currently no fix is available. - Please post on the aroma.affymetrix mailing list if you have problems using these files. [http://www.aroma-project.org/] - Files have been created in January 2013. * In case of available CEL files. Hope these are uselful! :) Regards, 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=qFHaMnoAAAAJ http://www.researcherid.com/rid/F-4912-2010 -- 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/
