Thank you Henrik Indeed the file GenomeWideSNP_6.Full.CDF is in the genomewidesnp6_libraryfile.zip on the Affymetrix website (it is still the same Apr 13 2007 file).
Best Steve > -----Original Message----- > From: aroma-affymetrix@googlegroups.com [mailto:aroma- > affymet...@googlegroups.com] On Behalf Of Henrik Bengtsson > Sent: December-01-11 12:56 PM > To: aroma-affymetrix@googlegroups.com > Subject: Re: [aroma.affymetrix] GenomeWideSNP_6 annotation file acquisition > issues > > Hi. > > On Thu, Dec 1, 2011 at 12:40 PM, Steven McKinney <smckin...@bccrc.ca> > wrote: > > Hi all, > > > > I am setting up to run analysis on Affymetrix SNP6, 250K Nsp and 250K Sty > chip types. > > As I read through the current documentation, I've noticed the following > items that > > may need attention, or I might need clarification: > > > > On page > > > > http://aroma-project.org/chipTypes/GenomeWideSNP_6 > > > > the hyperlinks at > > > > GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl > (GenomeWideSNP_6,na31,hg19,HB20110328.ufl) - Unit Fragment-Length (UFL) > annotation file > > > > GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl and > (GenomeWideSNP_6,na31,hg19,HB20110328.ufl) yield different file downloads, > > (namely GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl.gz and > GenomeWideSNP_6,na31,hg19,HB20110328.ufl.gz respectively) > > whereas the hyperlinks at > > > > GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp > (GenomeWideSNP_6,na31,hg19,HB20110328.ugp) - Unit Genome Position (UGP) > annotation file > > > > GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp and > (GenomeWideSNP_6,na31,hg19,HB20110328.ugp) both offer the same file > > > > GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp.gz > > Thanks. Correct now. > > > > > Also, I can not find where to access and download the files > > > > GenomeWideSNP_6.Full.CDF and GenomeWideSNP_6.CDF > > > > From what URL are these files available? > > These are available from Affymetrix, cf. 'Product Page' and > http://aroma-project.org/FAQ: > > FAQ. 2007-05-24: Where can I download CDF files > A: The CDF file for a given chip type is available in so called > "Library Files" at the corresponding "Support Materials" page on the > Affymetrix website. You may find links to those Affymetrix pages via > the Chip types pages. > > > > > (I have a copy of GenomeWideSNP_6.Full.cdf, of size 493291745 bytes dated > Apr 13 2007 - is this still valid > > or is there a newer version around?) > > Affymetrix CDF files more or less never changes, especially not for > DNA arrays. If they do, I'd expect them to change the names slightly, > for instance by adding a revision number. There might be so called > "custom CDFs" out there that others generated based on newer genome > annotations, but I am not aware of any for DNA arrays (there are lots > for expression arrays). > > /Henrik > > > > > > > Best > > > > Steve > > > > > > Steven McKinney, Ph.D. > > > > Statistician > > Molecular Oncology and Breast Cancer Program > > British Columbia Cancer Research Centre > > > > email: smckinney +at+ bccrc +dot+ ca > > > > tel: 604-675-8000 x7561 > > > > BCCRC > > Molecular Oncology > > 675 West 10th Ave, Floor 4 > > Vancouver B.C. > > V5Z 1L3 > > Canada > > > > -- > > 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/ -- 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/
