More below...
On Tue, Nov 9, 2010 at 1:16 PM, Henrik Bengtsson
<henrik.bengts...@aroma-project.org> wrote:
> 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
BTW, a good test to make sure it works for your genome, verify that
something like this works:
> db <- AromaGenomeTextFile$byGenome("Human");
> print(db);
AromaGenomeTextFile:
Name: Human
Tags: chromosomes
Full name: Human,chromosomes
Pathname: annotationData/genomes/Human/Human,chromosomes.txt
File size: 477 bytes
RAM: 0.01 MB
Number of data rows: 25
Columns [3]: 'chromosome', 'nbrOfBases', 'nbrOfGenes'
Number of text lines: 26
> data <- readDataFrame(db);
> print(data);
chromosome nbrOfBases nbrOfGenes
1 1 245203898 2968
2 2 243315028 2288
3 3 199411731 2032
4 4 191610523 1297
5 5 180967295 1643
6 6 170740541 1963
7 7 158431299 1443
8 8 145908738 1127
9 9 134505819 1299
10 10 135480874 1440
11 11 134978784 2093
12 12 133464434 1652
13 13 114151656 748
14 14 105311216 1098
15 15 100114055 1122
16 16 89995999 1098
17 17 81691216 1576
18 18 77753510 766
19 19 63790860 1454
20 20 63644868 927
21 21 46976537 303
22 22 49476972 288
23 X 152634166 1184
24 Y 50961097 231
25 M 16569 37
/Henrik
>
> 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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