MOUSEDIVm520650 and CRMAv2
Hans-Ulrich
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/880d164e7af6a849/3277e2d8870be696?lnk=gst&q=Mouse+diversity#3277e2d8870be696
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?
Best,
Hans-Ulrich
Henrik Bengtsson
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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>
Hans-Ulrich
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.
2) The ChromosomeExplorer() method does not work and it looks as if
the methods tries to generate plots for the human genome.
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?
Best wishes,
Hans-Ulrich
On Nov 5, 11:20 pm, Henrik Bengtsson <henrik.bengts...@aroma-
> 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:
Henrik Bengtsson
On Tue, Nov 9, 2010 at 3:37 AM, Hans-Ulrich
<hans-ulr...@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:
Hope this helps
Henrik
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
Henrik Bengtsson
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
Hans-Ulrich
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-
Henrik Bengtsson
before anything else, are you running the latest aroma.affymetrix
(v1.8.0), i.e. what's your sessionInfo()?
/Henrik
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
Hans-Ulrich
> 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-
> 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
>
>
> read more »
Henrik Bengtsson
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
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
Hans-Ulrich
I installed the patches and removed the report and the cbs folder.
Then, I run the segmentation and the chromosome explorer again. I got
the same/similar error message (see below). The error occured when
processing the second sample so the first one seems to run without
problems.
Can I run the chromosome explorer and exclude chromosome 25?
Regards,
Hans-Ulrich
20101206 12:53:52| Plotting S2 for chromosome 24 [NAMB]...done
20101206 12:53:52| Calling onFit.CopyNumberSegmentationModel()
hooks...done
20101206 12:53:52|Array #2 ('S2') of 4 on chromosome 24...done
20101206 12:53:52|Array #2 ('S2') of 4 on chromosome 25...
20101206 12:53:52| Loading results from file...
20101206 12:53:52| Pathname: cbsData/Koschmieder,ACC,ra,-XY,BPN,-
XY,RMA,A+B,FLN,-XY,paired/MOUSEDIVm520650/
S2,chr25,9012c8079b8a75fe8fc388ca02bfb65e.xdr
20101206 12:53:52| Fit object: DNAcopy
20101206 12:53:52| Loading results from file...done
20101206 12:53:52| Calling onFit.CopyNumberSegmentationModel()
hooks...
ERROR caught in onFit.CopyNumberSegmentationModel():
[2010-12-06 12:53:53] Exception: Cannot infer number of bases in
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)
at fcn(...)
at tryCatchOne(expr, names, parentenv, handlers[[1]])
at tryCatchList(expr, classes, parentenv, handlers)
at callHooks.list(hooks, ...)
at callHooks(hooks, ...)
at callHooks.default(hookName, fit = fit, chromosome = chr, fullname
= fullnam
at callHooks(hookName, fit = fit, chromosome = chr, fullname =
fullname)
at fit.CopyNumberSegmentationModel(this, ..., .retResults = FALSE,
verbose = v
at fit(this, ..., .retResults = FALSE, verbose = verbose)
at plot.CopyNumberSegmentationModel(model, path = path, imageFormat
= "png", p
at plot(model, path = path, imageFormat = "png", plotband =
plotband, arrays =
at writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes
= chromos
at writeGraphs(this, arrays = arrays, chromosomes = chromosomes,
zooms = zooms
at process.ChromosomeExplorer(ce, verbose = verbose)
at process(ce, verbose = verbose)
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 1178686 63 4079505 217.9 26615696 1421.5
Vcells 1568318 12 4818496 36.8 41974408 320.3
20101206 12:53:53| Calling onFit.CopyNumberSegmentationModel()
hooks...done
20101206 12:53:53|Calling onFit.CopyNumberSegmentationModel()
hooks...done
Error in list(`process(ce, verbose = verbose)` = <environment>,
`process.ChromosomeExplorer(ce, verbose = verbose)` =
<environment>, :
[2010-12-06 12:53:53] Exception: Cannot exit(): Argument 'indent'
makes 'indentPos' negative: -1
at throw(Exception(...))
at throw.default("Cannot exit(): Argument 'indent' makes 'indentPos'
negative:
at throw("Cannot exit(): Argument 'indent' makes 'indentPos'
negative: ", this
at exit.Verbose(verbose)
at exit(verbose)
at fit.CopyNumberSegmentationModel(this, ..., .retResults = FALSE,
verbose = v
at fit(this, ..., .retResults = FALSE, verbose = verbose)
at plot.CopyNumberSegmentationModel(model, path = path, imageFormat
= "png", p
at plot(model, path = path, imageFormat = "png", plotband =
plotband, arrays =
at writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes
= chromos
at writeGraphs(this, arrays = arrays, chromosomes = chromosomes,
zooms = zooms
at process.ChromosomeExplorer(ce, verbose = verbose)
at process(ce, verbose = verbose)
Error in list(`process(ce, verbose = verbose)` = <environment>,
`process.ChromosomeExplorer(ce, verbose = verbose)` =
<environment>, :
[2010-12-06 12:53:53] Exception: Cannot exit(): Argument 'indent'
makes 'indentPos' negative: -1
at throw(Exception(...))
at throw.default("Cannot exit(): Argument 'indent' makes 'indentPos'
negative:
at throw("Cannot exit(): Argument 'indent' makes 'indentPos'
negative: ", this
at exit.Verbose(this)
at exit(this)
at popState.Verbose(verbose)
at popState(verbose)
at throw.Exception(Exception(...))
at throw(Exception(...))
at throw.default("Cannot exit(): Argument 'indent' makes 'indentPos'
negative:
at throw("Cannot exit(): Argument 'indent' makes 'indentPos'
negative: ", this
at exit.Verbose(verbose)
at exit(verbose)
at fit.CopyNumberSegmentationModel(this, ..., .retResults = FALSE,
verbose = v
at fit(this, ..., .retResults = FALSE, verbose = verbose)
at plot.CopyNumberSegmentationModel(model, path = path, imageFormat
= "png", p
at plot(model, path = path, imageFormat = "png", plotband =
plotband, arrays =
at writeGraphs.ChromosomeExplore
20101206 12:53:53|Generating ChromosomeExplorer report...done
On Dec 3, 8:09 am, Henrik Bengtsson <henrik.bengts...@aroma-
project.org> wrote:
> Hi,
>
> 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
>
>
> read more »
Henrik Bengtsson
it looks like the patch wasn't applied. I've actually committed the
bug fix to CRAN where aroma.core v1.8.1 is now available. If you do
source("http://aroma-project.org/hbLite.R");
hbInstall("aroma.affymetrix");
that one should install (and any patches will be dropped).
Let me know if you still have problems
/Henrik
Hans-Ulrich
it works now without error messages! Thanks!
The chromosome explorer looks fine except for chromosomes > 19. There
are links for chromosomes 20,21,22 and X in the navigation bar that do
not work (since mice do not have chr. 20,21,22). Y and M are not
linked. I read in this forum that the links currently are "hard
coded". However, this is not a big problem for me.
Thanks,
Hans-Ulrich
On Dec 8, 1:37 am, Henrik Bengtsson <henrik.bengts...@aroma-
project.org> wrote:
> Hi,
>
> bug fix to CRAN where aroma.core v1.8.1 is now available. If you do
>
> source("http://aroma-project.org/hbLite.R");
> hbInstall("aroma.affymetrix");
>
> that one should install (and any patches will be dropped).
>
> Let me know if you still have problems
>
> /Henrik
>
> On Mon, Dec 6, 2010 at 4:54 AM, Hans-Ulrich
>
>
> read more »
Irsan Kooi
I am having the same problems with the chromosome explorer with mice as you have had. Can you send me the genome file you used to get the Chromosome explorer display mice cytobands in stead of human?
Irsan