Hi all, I am trying to use the "tilingArray" package to analyze Affymetrix S.pombe tiling arrays. I downloaded the .bpmap file from Affymetrix's website, and created a probeAnno object by bpmapToProbeAnno(). However, I am getting the following error when I try to segment the data by segChrom(). > segdf<-segChrom(cels,probeAnno,strands="NA") Running 'segment' on chromosome 1.NAError in probeAnno[w] : No mapping '1.NA.start' in this 'probeAnno' object. > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] davidTiling_1.2.12 GO.db_2.4.1 RSQLite_0.9-2 DBI_0.2-5 AnnotationDbi_1.10.2 tilingArray_1.26.0 pixmap_0.4-10 Starr_1.4.4 [9] affy_1.26.1 Ringo_1.12.0 Matrix_0.999375-39 lattice_0.18-8 limma_3.4.4 RColorBrewer_1.0-2 Biobase_2.8.0 affxparser_1.20.0 loaded via a namespace (and not attached): [1] affyio_1.16.0 annotate_1.26.1 genefilter_1.30.0 MASS_7.3-6 preprocessCore_1.10.0 pspline_1.0-14 splines_2.11.1 strucchange_1.4-1 [9] survival_2.35-8 tools_2.11.1 vsn_3.16.0 xtable_1.5-6 I am wondering if I used the correct .bpmap file?? Thanks for any suggestion/advice. -Sohail SBU, NY > [[alternative HTML version deleted]]

Dear Sohail in R, the character string "NA" is different from the value NA. Try with supplying the second one for the argument 'strands'. Also, please make sure that the 'chr' argument is set to the right value, the default (1:17) is likely not to work with S.pombe. You can see what the chromosome names are in your organism by inspecting the probeAnno object. Best wishes Wolfgang On Sep/8/10 10:33 PM, sohkhan at notes.cc.sunysb.edu wrote: > Hi all, > > I am trying to use the "tilingArray" package to analyze Affymetrix S.pombe > tiling arrays. I downloaded the .bpmap file from Affymetrix's website, > and created a probeAnno object by bpmapToProbeAnno(). > However, I am getting the following error when I try to segment the data > by segChrom(). > >> segdf<-segChrom(cels,probeAnno,strands="NA") > Running 'segment' on chromosome 1.NAError in probeAnno[w] : > No mapping '1.NA.start' in this 'probeAnno' object. > >> sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] davidTiling_1.2.12 GO.db_2.4.1 RSQLite_0.9-2 DBI_0.2-5 > AnnotationDbi_1.10.2 tilingArray_1.26.0 pixmap_0.4-10 Starr_1.4.4 > > [9] affy_1.26.1 Ringo_1.12.0 Matrix_0.999375-39 > lattice_0.18-8 limma_3.4.4 RColorBrewer_1.0-2 Biobase_2.8.0 > affxparser_1.20.0 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 annotate_1.26.1 genefilter_1.30.0 > MASS_7.3-6 preprocessCore_1.10.0 pspline_1.0-14 splines_2.11.1 > strucchange_1.4-1 > [9] survival_2.35-8 tools_2.11.1 vsn_3.16.0 xtable_1.5-6 > > > I am wondering if I used the correct .bpmap file?? > Thanks for any suggestion/advice. > > -Sohail > SBU, NY >> > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber

Hello Sohail, > How can I run the segmentation for chromosomes 1:3? I would try this: chr = c("Sp...chr1","Sp.....chr2","Sp.....chr3") > How do I define the strands parameter? 0 and 1 for strand info? hmmm... I have not seen this in my limited experience but would try something like this: strands = c("0") strands = c("0", "1") I am not sure though if the creation of the probeAnno object from the BPMAP file treated those 0 and 1 as character vectors. I suspect that the bpmapTo ProbeAnno function already took care of the 0 and 1 strand info. Maybe someone else can chime in since I don't have R fired up right now. If during the creation of the probeAnno object the zero and one were converted then you can use: strands = c("+", "-") You should be able to explore the probeAnno object to check this nomenclature. Best, noah On Sep 13, 2010, at 5:44 PM, sohkhan@notes.cc.sunysb.edu wrote: > Hi Noah, > > Thanks. Supplying the chr parameter as "Sp....chr1" works. How can I run the segmentation for chromosomes 1:3? chr="Sp...chr1":"Sp.....chr3" doesn't work. > Second, BPMAP file has 0's and 1's for the strand column. Is 0 = - and 1= +? How do I define the strands parameter? > Thank you. > > -Sohail > -----Noah Dowell <noahd@ucla.edu> wrote: ----- > > To: sohkhan@notes.cc.sunysb.edu > From: Noah Dowell <noahd@ucla.edu> > Date: 09/10/2010 02:00PM > Subject: Re: [BioC] probeAnno for tilingArray package. > > Hello Sohail, > > I am certainly not the expert on the tilingArray package but this seems similar to an error I encountered. Did you search the archives? > > Here are some suggestions for troubleshooting: > > 1. The Affymetrix S. cerevisiae bpmap does not use the "1.NA.start" annotation for the chromosomes. Instead they use an annotation like this: > > "Sc:Oct_2003;chr1" > > I suspect that is similar to the annotation in your probeAnno object therefore the result of the segChrom function not finding a mapping for "1.NA.start" > The chromosome names probably printed to the screen after you ran bpmapToProbeAnno unless you changed the defaults. > > 2. How does one fix this error? How did you create your "cels" object that you passed to the segChrom function? It needs to be an Expression Set. You can create this using the readCelFile function in the Starr package. > > 3. You may also want to try to define the "chr" variable in the segChrom function. I would do something like this: > > segData = segChrom(DataeSet, probeAnno, chr= "Sc:Oct_2003;chr1", strands = c("-")) > > HTH, > > noah > > On Sep 8, 2010, at 1:33 PM, sohkhan@notes.cc.sunysb.edu wrote: > > > Hi all, > > > > I am trying to use the "tilingArray" package to analyze Affymetrix S.pombe > > tiling arrays. I downloaded the .bpmap file from Affymetrix's website, > > and created a probeAnno object by bpmapToProbeAnno(). > > However, I am getting the following error when I try to segment the data > > by segChrom(). > > > >> segdf<-segChrom(cels,probeAnno,strands="NA") > > Running 'segment' on chromosome 1.NAError in probeAnno[w] : > > No mapping '1.NA.start' in this 'probeAnno' object. > > > >> sessionInfo() > > R version 2.11.1 (2010-05-31) > > x86_64-apple-darwin9.8.0 > > > > locale: > > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > [1] grid stats graphics grDevices utils datasets methods > > base > > > > other attached packages: > > [1] davidTiling_1.2.12 GO.db_2.4.1 RSQLite_0.9-2 DBI_0.2-5 > > AnnotationDbi_1.10.2 tilingArray_1.26.0 pixmap_0.4-10 Starr_1.4.4 > > > > [9] affy_1.26.1 Ringo_1.12.0 Matrix_0.999375-39 > > lattice_0.18-8 limma_3.4.4 RColorBrewer_1.0-2 Biobase_2.8.0 > > affxparser_1.20.0 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.16.0 annotate_1.26.1 genefilter_1.30.0 > > MASS_7.3-6 preprocessCore_1.10.0 pspline_1.0-14 splines_2.11.1 > > strucchange_1.4-1 > > [9] survival_2.35-8 tools_2.11.1 vsn_3.16.0 xtable_1.5-6 > > > > > > I am wondering if I used the correct .bpmap file?? > > Thanks for any suggestion/advice. > > > > -Sohail > > SBU, NY > >> > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]

On Sep/14/10 7:36 PM, sohkhan at notes.cc.sunysb.edu wrote: > Thank you Wolfgang. > I corrected the chr parameter as suggested by Noah. segChrom runs with > strand=NA. Now, I have question about the probeAnno creation by > bpmapToProbeAnno(). Does the function treat 0's as "-" and 1's "+" strand. > I have just one BPMAP file for S.pombe from Affymetrix which contains > 0's and 1's in the strand column. Why don't you just try and report problems, if any? Wolfgang > Thanks again. > -Sohail > > > > From: Wolfgang Huber <whuber at="" embl.de=""> > To: bioconductor at stat.math.ethz.ch > Date: 09/11/2010 08:15 AM > Subject: Re: [BioC] probeAnno for tilingArray package. > Sent by: bioconductor-bounces at stat.math.ethz.ch > -------------------------------------------------------------------- ---- > > > > Dear Sohail > > in R, the character string "NA" is different from the value NA. Try with > supplying the second one for the argument 'strands'. Also, please make > sure that the 'chr' argument is set to the right value, the default > (1:17) is likely not to work with S.pombe. You can see what the > chromosome names are in your organism by inspecting the probeAnno object. > > Best wishes > Wolfgang > > On Sep/8/10 10:33 PM, sohkhan at notes.cc.sunysb.edu wrote: > > Hi all, > > > > I am trying to use the "tilingArray" package to analyze Affymetrix > S.pombe > > tiling arrays. I downloaded the .bpmap file from Affymetrix's website, > > and created a probeAnno object by bpmapToProbeAnno(). > > However, I am getting the following error when I try to segment the data > > by segChrom(). > > > >> segdf<-segChrom(cels,probeAnno,strands="NA") > > Running 'segment' on chromosome 1.NAError in probeAnno[w] : > > No mapping '1.NA.start' in this 'probeAnno' object. > > > >> sessionInfo() > > R version 2.11.1 (2010-05-31) > > x86_64-apple-darwin9.8.0 > > > > locale: > > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > [1] grid stats graphics grDevices utils datasets methods > > base > > > > other attached packages: > > [1] davidTiling_1.2.12 GO.db_2.4.1 RSQLite_0.9-2 DBI_0.2-5 > > AnnotationDbi_1.10.2 tilingArray_1.26.0 pixmap_0.4-10 Starr_1.4.4 > > > > [9] affy_1.26.1 Ringo_1.12.0 Matrix_0.999375-39 > > lattice_0.18-8 limma_3.4.4 RColorBrewer_1.0-2 Biobase_2.8.0 > > affxparser_1.20.0 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.16.0 annotate_1.26.1 genefilter_1.30.0 > > MASS_7.3-6 preprocessCore_1.10.0 pspline_1.0-14 splines_2.11.1 > > strucchange_1.4-1 > > [9] survival_2.35-8 tools_2.11.1 vsn_3.16.0 xtable_1.5-6 > > > > > > I am wondering if I used the correct .bpmap file?? > > Thanks for any suggestion/advice. > > > > -Sohail > > SBU, NY > >> > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > 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 > > -- > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > 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 > -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber