Hi,
I could reproduce this error (also on the Human genome when trying to
generate CE plots for Chr25). It's a bug, which I have patched (until
next release). Run the following and the patches will be installed
too:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
Let me know if it solves your problem.
/Henrik
On Wed, Dec 1, 2010 at 2:28 PM, Hans-Ulrich
<hans-ulrich.kl...@uni-muenster.de> wrote:
> 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.
>
>
> 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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