[aroma.affymetrix] Re: MOUSEDIVm520650 and CRMAv2
Hi Hans-Ulrich, 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 -- 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/
[aroma.affymetrix] Re: MOUSEDIVm520650 and CRMAv2
Hi Hendrik,
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,
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
On Mon, Dec 6, 2010 at 4:54 AM, Hans-Ulrich
hans-ulrich.kl...@uni-muenster.de wrote:
Hi Hendrik,
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
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)
at tryCatch({
at fcn(...)
at doTryCatch(return(expr), name, parentenv, handler)
at tryCatchOne(expr, names, parentenv, handlers[[1]])
at tryCatchList(expr, classes, parentenv, handlers)
at tryCatch({
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,
Re: [aroma.affymetrix] Re: MOUSEDIVm520650 and CRMAv2
Hi,
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
On Mon, Dec 6, 2010 at 4:54 AM, Hans-Ulrich
hans-ulrich.kl...@uni-muenster.de wrote:
Hi Hendrik,
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
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)
at tryCatch({
at fcn(...)
at doTryCatch(return(expr), name, parentenv, handler)
at tryCatchOne(expr, names, parentenv, handlers[[1]])
at tryCatchList(expr, classes, parentenv, handlers)
at tryCatch({
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
[aroma.affymetrix] Re: MOUSEDIVm520650 and CRMAv2
Hi Hendrik,
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
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)
at tryCatch({
at fcn(...)
at doTryCatch(return(expr), name, parentenv, handler)
at tryCatchOne(expr, names, parentenv, handlers[[1]])
at tryCatchList(expr, classes, parentenv, handlers)
at tryCatch({
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 634079505 217.9 26615696 1421.5
Vcells 1568318 124818496 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
[aroma.affymetrix] Re: MOUSEDIVm520650 and CRMAv2
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 121257530712 13 120284312850 14 125194864860 15 103494974823 16 98319150679 17 95272651 1075 18 90772031522 19 61342430739 23 166650296800 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
Re: [aroma.affymetrix] Re: MOUSEDIVm520650 and CRMAv2
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
[aroma.affymetrix] Re: MOUSEDIVm520650 and CRMAv2
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.
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-
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$byChipType(chipType);
# Get the pathname of the source file
pathname - getPathname(ufl);
# Create pathname of new file
path - getPath(ufl);
tags - getTags(ufl);
tags - grep(HB, tags, value=TRUE, invert=TRUE); # Drop HB2010 tag
tags - c(tags, filter45-2000, HB20101105);
fullname - paste(c(chipType, tags), collapse=,);
filename - sprintf(%s.ufl, fullname);
pathnameD - file.path(path, filename);
copyFile(pathname, pathnameD);
# Filter values
uflD - AromaUflFile$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
--
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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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Re: [aroma.affymetrix] Re: MOUSEDIVm520650 and CRMAv2
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/9593afed0d424450/d4e9de835c224db8
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 HB2010 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 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/
--
Re: [aroma.affymetrix] Re: MOUSEDIVm520650 and CRMAv2
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/9593afed0d424450/d4e9de835c224db8 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 114151656748 14 14 105311216 1098 15 15 100114055 1122 16 16 89995999 1098 17 17 81691216 1576 18 18 77753510766 19 19 63790860 1454 20 20 63644868927 21 21 46976537303 22 22 49476972288 23 X 152634166 1184 24 Y 50961097231 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 HB2010 tag tags - c(tags, filter45-2000, HB20101105); fullname - paste(c(chipType, tags), collapse=,); filename - sprintf(%s.ufl, fullname); pathnameD -
