Sorry, I forgot that:
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] Cairo_1.4-5 RColorBrewer_1.0-2
DNAcopy_1.24.0
[4] preprocessCore_1.12.0 sfit_0.1.9
aroma.affymetrix_1.8.1
[7] aroma.apd_0.1.7 affxparser_1.22.0
R.huge_0.2.0
[10] aroma.core_1.8.0 aroma.light_1.18.2
matrixStats_0.2.2
[13] R.rsp_0.4.0 R.cache_0.3.0
R.filesets_0.9.1
[16] digest_0.4.2 R.utils_1.5.8
R.oo_1.7.4
[19] R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] tools_2.12.0
Warning message:
'DESCRIPTION' file has 'Encoding' field and re-encoding is not
possible
Regards,
Hans-Ulrich
On Dec 1, 6:44 pm, Henrik Bengtsson <henrik.bengts...@aroma-
project.org> wrote:
> 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
>
> ...
>
> read more »
--
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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