Hi.
On Tue, Nov 9, 2010 at 3:37 AM, Hans-Ulrich
<hans-ulrich.kl...@uni-muenster.de> wrote:
> Hi Henrik,
>
> thank you very much for your help! I tried your code and it seemed
> that I got reasonable results. I will compare the results to the
> results from the Affymetrix software later, but it looks well at a
> first glance.
>
> I have two other questions/remarks:
> 1) The data.frames returned by getRegions() on the segmented copy
> numbers contains links to the human genome and not to the mouse
> genome.
That's unfortunately still hardwired and has to be manually edited afterwards.
> 2) The ChromosomeExplorer() method does not work and it looks as if
> the methods tries to generate plots for the human genome.
Does the "and" mean "because" here or are there two different problems?
>
> Both issues are not serious and I could fix 1) quickly using the gsub
> command. However, can I pass the mouse genome as parameter or are
> these functions implemented for the human genome only?
It is possible to specify which genome the segmentation method should
use and hence ChromosomeExplorer. For this to work you need to
provide correctly formatted genome annotation data under
annotationData/genomes/<GenomeName>/. For an example of such a file,
see
path <- system.file("annotationData/genomes/Human", package="aroma.core");
filename <- "Human,chromosomes.txt";
pathname <- file.path(path, filename);
file.show(pathname);
Also, have a look at thread 'Custom Canine SNP (DogSty06m520431);
problem with chr24-39 Options' started on August 23, 2010:
https://groups.google.com/group/aroma-affymetrix/browse_thread/thread/9593afed0d424450/d4e9de835c224db8
Hope this helps
Henrik
>
> Best wishes,
> Hans-Ulrich
>
>
> On Nov 5, 11:20 pm, Henrik Bengtsson <henrik.bengts...@aroma-
> project.org> wrote:
>> 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/...
>>
>> > 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.
>>
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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.
>
>
> 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
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