Hi. On Fri, Nov 5, 2010 at 9:09 AM, Hans-Ulrich <hans-ulrich.kl...@uni-muenster.de> wrote: > Hi all, > > I am using the Affymetrix "MOUSEDIVm520650" chip. During the the > normalization step for fragment length, the aroma software complains > that no probes for enzyme 1 only exist (the same for enzyme 2). I > found > this discussion: > http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/880d164e7af6a849/3277e2d8870be696?lnk=gst&q=Mouse+diversity#3277e2d8870be696 > > > In the NetAffx annotation files, all probes have fragment length for > both enzymes, although they are sometimes quite large. The affymetrix > protocol says that the PCR works well for fragments between 200 and > 1100bps. The annotation files for the Genome Wide SNP 6.0 arrays > annotate fragments up to 2000bps. > > To use the aroma software, I want to modify the ufl file and set all > fragment length entries < 45 or > 2000 to NA. Unfortunately, I have > no > plan how to do this. Can someone point me to appropriate > documentation?
The how-to page 'Create a Unit Fragment Length (UFL) file' at http://aroma-project.org/howtos/CreateAUnitFragmentLengthFile should be useful. Make sure to not update the original UFL file, but instead a renamed copy of it. Bah, it's easier if I just write it: # Get the UFL file chipType <- "MOUSEDIVm520650"; ufl <- AromaUflFile$byChipType(chipType); # Get the pathname of the source file pathname <- getPathname(ufl); # Create pathname of new file path <- getPath(ufl); tags <- getTags(ufl); tags <- grep("HB", tags, value=TRUE, invert=TRUE); # Drop HB2010xxxx tag tags <- c(tags, "filter45-2000", "HB20101105"); fullname <- paste(c(chipType, tags), collapse=","); filename <- sprintf("%s.ufl", fullname); pathnameD <- file.path(path, filename); copyFile(pathname, pathnameD); # Filter values uflD <- AromaUflFile$byChipType(chipType, tags=tags); for (cc in nbrOfColumns(uflD)) { fl <- ufl[,cc]; idxs <- which(fl < 450 | fl > 2000); uflD[idxs,cc] <- NA; } # for (cc ...) # Update file footer ftr <- readFooter(uflD); srcFile <- list(filename=getFilename(ufl), filesize=getFileSize(ufl), checksum=getChecksum(ufl)); ftr$srcFiles <- list(srcFile=srcFile)); writeFooter(uflD, ftr); That should be it. /Henrik > > Best, > 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/
