Hi Hendrik. Sure - I would like to share my annotation files. I made a new .ugp file without problems. Unfortunately, a known issue arises when creating the new .ufl file. When importing the ufl information from the NetAffx annotation files na31, the following warning appears:
Warning messages: 1: In updateDataColumn.AromaTabularBinaryFile(this, .con = con, .hdr = hdr, : 4 values to be assigned were out of range [-32768,32767] and therefore censored to fit the range. Of these, 4 values in [42148,51916] were too large. 2: In updateDataColumn.AromaTabularBinaryFile(this, .con = con, .hdr = hdr, : 90 values to be assigned were out of range [-32768,32767] and therefore censored to fit the range. Of these, 90 values in [33603,21059245] were too large. Actually, some frangments are really very large (and other are very small): > summary(ufl) length length.02 Min. : 7 Min. : 7 1st Qu.: 432 1st Qu.: 755 Median : 679 Median : 1433 Mean : 923 Mean : 1922 3rd Qu.: 976 3rd Qu.: 2609 Max. :32767 Max. :32767 NA's :29333 NA's :15585 This is different from annotation version na30. (The same issue came up with the Mouse Diversity Array. I wrote that in another thread.) Instead of modifying the annotation files and setting fragment length > 2000 to NA etc., I would prefer to keep the original annotation and add a parameter to the function for fragment length normalization (max and min fragment length). What do you think? Also, I will write to the affymetrix forum and ask why they changed their annotation. Best, Hans-Ulrich On Dec 10, 5:49 pm, Henrik Bengtsson <henrik.bengts...@aroma- project.org> wrote: > 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 websitehttp://www.aroma-project.org/. > > To post to this group, send email to aroma-affymetrix@googlegroups.com > > To unsubscribe and other options, go tohttp://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/
