Question: Reading .bpmap files for homemade tiling arrays
0
gravatar for Larry Singh
9.6 years ago by
Larry Singh20
Larry Singh20 wrote:
Patrick Schorderet <patrick.schorderet at="" ...=""> writes: > > > Hello everybody, > > I am trying to normalize some ChIP-chip data using rMAT and to do so, > you have to feed your .bpmap to the program (the file contains > information relating to the design of the Affymetrix tiling arrays). > Unfortunately, I get an error saying I am working with doubles instead > of the wanted integer. I have not changed the .bpmap file at all and I > can make no sense of it because have nothing to open it properly. I > guess it might be due to the customized array we are using. The sizes > might be different? > > Thanks for the help, > > Patrick [ ... deleted ] Patrick, I had a similar problem, and after some debugging I discovered that you must enter a valid groupName when calling BPMAPCelParser. You can get a list of the group names in the bpmap file by just looking at bpmapA$GroupName. I'm not sure this will solve your problem but perhaps it will. Hope this helps, -Larry.
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ADD COMMENTlink modified 9.6 years ago by Raphael Gottardo40 • written 9.6 years ago by Larry Singh20
Answer: Reading .bpmap files for homemade tiling arrays
0
gravatar for Noah Dowell
9.6 years ago by
Noah Dowell410
Noah Dowell410 wrote:
Hello Patrick, I don't know what your setup is but when I am dealing with unknown files then the simple Unix command: head <filename> in a terminal window (or Unix interpreter) will give me the top ten lines of the file and then I can figure out what columns I need. I thought I used that on some bpmap files a while back but maybe I am misremembering. Also the Ringo and Starr packages have a function to read bpmap files which you could you to read in and then explore the file... best, noah On May 17, 2010, at 5:33 PM, Larry Singh wrote: > Patrick Schorderet <patrick.schorderet at="" ...=""> writes: > >> >> >> Hello everybody, >> >> I am trying to normalize some ChIP-chip data using rMAT and to do so, >> you have to feed your .bpmap to the program (the file contains >> information relating to the design of the Affymetrix tiling arrays). >> Unfortunately, I get an error saying I am working with doubles instead >> of the wanted integer. I have not changed the .bpmap file at all and I >> can make no sense of it because have nothing to open it properly. I >> guess it might be due to the customized array we are using. The sizes >> might be different? >> >> Thanks for the help, >> >> Patrick > > [ ... deleted ] > > Patrick, > > I had a similar problem, and after some debugging I discovered that you must > enter a valid groupName when calling BPMAPCelParser. You can get a list of the > group names in the bpmap file by just looking at bpmapA$GroupName. I'm not > sure this will solve your problem but perhaps it will. > > Hope this helps, > -Larry. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 9.6 years ago by Noah Dowell410
Answer: Reading .bpmap files for homemade tiling arrays
0
gravatar for Raphael Gottardo
9.6 years ago by
Raphael Gottardo40 wrote:
Hi Larry and Patrick, Sorry for the late reply. Indeed, it is most likely the error that Larry reported. I have included a test to make sure that the groupName is valid. It should appear in the devel version, as ?of rMAT 2.5.1.? If things go well, I will push it to the Branch release next week. It's a minor fix. In the meantime please make sure your groupName is valid.? Best, Raphael On 2010-05-17, at 8:33 PM, Larry Singh wrote: Patrick Schorderet <patrick.schorderet at="" ...=""> writes: Hello everybody, I am trying to normalize some ChIP-chip data using rMAT and to do so, ? you have to feed your .bpmap to the program (the file contains ? information relating to the design of the Affymetrix tiling arrays). ? Unfortunately, I get an error saying I am working with doubles instead ? of the wanted integer. I have not changed the .bpmap file at all and I ? can make no sense of it because have nothing to open it properly. I ? guess it might be due to the customized array we are using. The sizes ? might be different? Thanks for the help, Patrick [ ... deleted ] Patrick, I had a similar problem, and after some debugging I discovered that you must enter a valid groupName when calling BPMAPCelParser. ?You can get a list of the group names in the bpmap file by just looking at bpmapA$GroupName ?I'm not sure this will solve your problem but perhaps it will. Hope this helps, -Larry. _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 9.6 years ago by Raphael Gottardo40
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