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/
