Hi,
before anything else, are you running the latest aroma.affymetrix
(v1.8.0), i.e. what's your sessionInfo()?
/Henrik
On Wed, Dec 1, 2010 at 9:32 AM, Hans-Ulrich
<hans-ulrich.kl...@uni-muenster.de> wrote:
> Hi Hendrik,
>
> I created a file for the mouse genome. However, I still get an error
> message:
>
>> cbs = CbsModel(cesNSamples, cesNControls, genome="Mouse")
>> df <- getGenomeData(cbs, verbose=verbose)
> 20101201 14:44:53|Reading genome chromosome annotation file...
> 20101201 14:44:53| Searching for the file...
> 20101201 14:44:54| Searching for the file...done
> 20101201 14:44:54| Reading data file...
> 20101201 14:44:54| Pathname: annotationData/genomes/Mouse/
> Mouse,chromosomes.txt
> 20101201 14:44:54| Reading data file...done
> 20101201 14:44:54| Translating chromosome names...
> 20101201 14:44:54| Translating chromosome names...done
> 20101201 14:44:54|Reading genome chromosome annotation file...done
>> df
> nbrOfBases nbrOfGenes
> 1 197195432 1237
> 2 181748087 1779
> 3 159599783 1046
> 4 155630120 1286
> 5 152537259 1285
> 6 149517037 1158
> 7 152524553 1975
> 8 131738871 1082
> 9 124076172 1260
> 10 129993255 1036
> 11 121843856 1606
> 12 121257530 712
> 13 120284312 850
> 14 125194864 860
> 15 103494974 823
> 16 98319150 679
> 17 95272651 1075
> 18 90772031 522
> 19 61342430 739
> 23 166650296 800
> 24 15902555 12
> M 16299 13
>> fit(cbs, min.width=5, verbose=verbose)
>> ce = ChromosomeExplorer(cbs)
>> process(ce, verbose=verbose)
> [...]
> ERROR caught in onFit.CopyNumberSegmentationModel():
> [2010-12-01 18:18:04] Exception: Cannot infer number of bases in
> chromosome. No such chromosome: 25
> at throw(Exception(...))
> at throw.default("Cannot infer number of bases in chromosome. No
> such chromoso
> at throw("Cannot infer number of bases in chromosome. No such
> chromosome: ", c
> at getChromosomeLength(chromosome)
> at doTryCatch(return(expr), name, parentenv, handler)
> at tryCatchOne(expr, names, parentenv, handlers[[1]])
> at tryCatchList(expr, classes, parentenv, handlers)
> [...]
>
> Do I have to rename chromosome "M" to "25"?
>
>
> Best wishes,
> Hans-Ulrich
>
>
> On Nov 9, 10:20 pm, Henrik Bengtsson <henrik.bengts...@aroma-
> project.org> wrote:
>> 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...
>>
>> 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.
>>
>> >>> > 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 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/
>
--
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/
