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
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