Hi. On Fri, Dec 10, 2010 at 3:04 AM, Hans-Ulrich <hans-ulrich.kl...@uni-muenster.de> wrote: > Hi all. > > I want to apply CRMAv2 + CBS to Genome Wide SNP 6.0 arrays. The > segments created by CBS should have hg19 coordinates. I looked at the > aroma project web site: > http://www.aroma-project.org/chipTypes/GenomeWideSNP_6 > > The annotation files are based on na30 and hg18. I probably can create > a new .ugp and .ufl file for hg19 based on the R scripts available on > that page.
If you create these, would mind sharing them with others? I can make them available on the chip type page. See also links below. > However, there is no script for the .acs file. There is; see below. > So, I have two questions: > > What is stored in these annotation files? > - .ufl -- length of the fragments (?) > - .ugp -- mapping from probes to genomic positions (?) > - .acs -- mapping from probes to sequences (?) > > If my guesses above are correct, can create new .ufl and .ugp files > and use the old .acs file? Correct, since the sequences on the actually chip never changes, the Aroma Cell Sequence (ACS) file is not changing either. An exception is when we obtain sequences for cells for which we did not them before. See Section 'Building custom-made annotation data' on http://aroma-project.org/howtos for more details on how to build UFL and UGP (and ACS). /Henrik > > Thanks, > Hans-Ulrich > > -- > 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/
