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=gstq=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$byChipType(chipType);
# Get the pathname of the source file
pathname - getPathname(ufl);
# Create pathname of new file
path - getPath(ufl);
tags - getTags(ufl);
tags - grep(HB, tags, value=TRUE, invert=TRUE); # Drop HB2010 tag
tags - c(tags, filter45-2000, HB20101105);
fullname - paste(c(chipType, tags), collapse=,);
filename - sprintf(%s.ufl, fullname);
pathnameD - file.path(path, filename);
copyFile(pathname, pathnameD);
# Filter values
uflD - AromaUflFile$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
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--
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.
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