Ringo package: error using computeRunningMedians function
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Diego Villar ▴ 40
@diego-villar-3649
Last seen 10.2 years ago
Dear All, I am trying to use Ringo for analysis of Agilent platform ChIP-chip. I get the following output/error when applying the computeRunningMedians function to my expression set (2 samples, one normal and one dye- swap): Chromosome 1 ... 170809ds ... 261108no ... Chromosome 10 ... 170809ds ... 261108no ... Chromosome 11 ... 170809ds ... Error en newExprs[chridx, i] <- chrrm : NAs are not allowed in subscribed assignations Does this mean missing values are not allowed at all for this function? How could I modify my input so that the function would work on my data? Would I need to substite NAs somehow in the ExpressionSet? Thanks in advance for your time and help, Diego Villar Diego Villar Laboratorio 2.5.2 Tel?fono 915854442 Instituto de Investigaciones Biom?dicas "Alberto Sols" CArturo Duperier, 4 28029 Madrid
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@joern-toedling-3465
Last seen 10.2 years ago
Hello, I'm afraid I do not understand the error message. NAs in your ExpressionSet should not be a problem. I suspect that the problem might be with your probeAnno object, especially with the probes on chromosome 11 (since it seems to work with chromosomes 1 and 10). How did you build the probeAnno object? Assuming your probeAnno object is called P, what is the output of validObject(P) str(P["11.start"]) str(P["11.index"]) ? And please always remember to add the result of typing "sessionInfo()" in your R to any question you ask on this list, as this allows us to see which software versions you are using. Regards, Joern On Mon, 31 Aug 2009 11:48:17 +0000, Diego Villar wrote > Dear All, > > I am trying to use Ringo for analysis of Agilent platform ChIP- > chip. I get the following output/error when applying the computeRunningMedians > function to my expression set (2 samples, one normal and one dye- > swap): > > Chromosome 1 ... > 170809ds ... 261108no ... > Chromosome 10 ... > 170809ds ... 261108no ... > Chromosome 11 ... > 170809ds ... Error en newExprs[chridx, i] <- chrrm : > NAs are not allowed in subscribed assignations > > Does this mean missing values are not allowed at all for this > function? How could I modify my input so that the function would > work on my data? Would I need to substite NAs somehow in the ExpressionSet? > > Thanks in advance for your time and help, > > Diego Villar > --- Joern Toedling Institut Curie -- U900 26 rue d'Ulm, 75005 Paris, FRANCE Tel. +33 (0)156246926
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Hello, Joern: Thanks a lot for your prompt reply. *** How did you build the probeAnno object? *** I build the ProbeAnno object from a table resembling a pos file, using the following: ProbeAnno<- posToProbeAnno("alt_prom_array.pos", chrNameColumn = "CHROMOSOME", probeColumn = "Name", chrPositionColumn = "POSITION", lengthColumn = "LENGTH", sep="\t", genome="H.Sapiens (hg17)", microarrayPlatform="Agilent alt prom array (custom)") The pos file I used is a tab delimited text file which looks like: Name ID CHROMOSOME POSITION COUNT LENGTH chrX.71280574.71280634 FLJ44635_71280558_16 chrX 71280574 1 60 chr10.116034763.116034823 VWA2_116034286_477 chr10 116034763 1 60 chr11.383389.383449 PKP3_383245_144 chr11 383389 1 60 I built it this way since the array is an old Agilent custom array (hg17) and the function that you propose in the Ringo script for creating a probeAnno object from the genes section of an RG did not work on my data. The probeAnno generated in this way works fine with chipAlongChrom function on a region of chromosome 11, but after that I get the mentioned error when using computeRunningMedians. chipAlongChrom(eSet, chrom="11", xlim=c(18371851,18373350), ylim=c(-2,4), probeAnno=ProbeAnno, gff=gff) smoothX <- computeRunningMedians(eSet, probeAnno=ProbeAnno, modColumn = "Cy5", winHalfSize = 400) *** Assuming your probeAnno object is called P,what is the output of validObject(P), str(P["11.start"]) str(P["11.index"])? *** > validObject(ProbeAnno) [1] TRUE > str(ProbeAnno["11.start"]) int [1:16314] 186565 186773 186844 186910 189356 189422 189471 189516 189604 279308 ... > str(ProbeAnno["11.index"]) chr [1:16314] "chr11.186565.186625" "chr11.186773.186833" ... *** And please always remember to add the result of typing "sessionInfo()" in your R to any question you ask on this list, as this allows us to see which software versions you are using *** > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=Spanish_Spain.1252;LC_CTYPE=Spanish_Spain.1252;LC_MONETARY= Spanish_Spain.1252;LC_NUMERIC=C;LC_TIME=Spanish_Spain.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Ringo_1.8.0 Matrix_0.999375-24 lattice_0.17-22 limma_2.18.2 [5] RColorBrewer_1.0-2 Biobase_2.4.1 loaded via a namespace (and not attached): [1] annotate_1.22.0 AnnotationDbi_1.6.0 DBI_0.2-4 [4] genefilter_1.24.0 grid_2.9.0 RSQLite_0.7-1 [7] splines_2.9.0 survival_2.35-4 tools_2.9.0 [10] xtable_1.5-5 Thanks again for your help, Diego Con fecha 31/8/2009, "Joern Toedling" <joern.toedling at="" curie.fr=""> escribi?: >Hello, > >I'm afraid I do not understand the error message. NAs in your ExpressionSet >should not be a problem. I suspect that the problem might be with your >probeAnno object, especially with the probes on chromosome 11 (since it seems >to work with chromosomes 1 and 10). How did you build the probeAnno object? >Assuming your probeAnno object is called P, >what is the output of >validObject(P) >str(P["11.start"]) >str(P["11.index"]) >? And please always remember to add the result of typing "sessionInfo()" in >your R to any question you ask on this list, as this allows us to see which >software versions you are using. > >Regards, >Joern > >On Mon, 31 Aug 2009 11:48:17 +0000, Diego Villar wrote >> Dear All, >> >> I am trying to use Ringo for analysis of Agilent platform ChIP- >> chip. I get the following output/error when applying the computeRunningMedians >> function to my expression set (2 samples, one normal and one dye- >> swap): >> >> Chromosome 1 ... >> 170809ds ... 261108no ... >> Chromosome 10 ... >> 170809ds ... 261108no ... >> Chromosome 11 ... >> 170809ds ... Error en newExprs[chridx, i] <- chrrm : >> NAs are not allowed in subscribed assignations >> >> Does this mean missing values are not allowed at all for this >> function? How could I modify my input so that the function would >> work on my data? Would I need to substite NAs somehow in the ExpressionSet? >> >> Thanks in advance for your time and help, >> >> Diego Villar >> > > >--- >Joern Toedling >Institut Curie -- U900 >26 rue d'Ulm, 75005 Paris, FRANCE >Tel. +33 (0)156246926 > Diego Villar Laboratorio 2.5.2 Tel?fono 915854442 Instituto de Investigaciones Biom?dicas "Alberto Sols" CArturo Duperier, 4 28029 Madrid
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Well, this looks all fine to me. I cannot tell you immediately where the problem is, and since I have not run into such an error before, we'll have to search for the source of the problem together. The fact that chromosomes 1 and 10 work but chromosome 11 does not strongly suggests that there is something unusual with the elements of that chromosome 11 in the probeAnno object. Further things we can check: table(ProbeAnno["11.unique"]) table(ProbeAnno["11.index"] %in% featureNames(eSet)) Otherwise, consider setting options(error=recover) then when the error occurs, type the frame number of'computeRunningMedians' and please tell me what the result of str(chridx) str(i) str(chrrm) are. Alternatively, if you don't mind you could save the objects eSet and ProbeAnno into a file (using command 'save') and provide them somewhere to me for downloading. I could check these things myself then. Regards, Joern On Mon, 31 Aug 2009 14:55:41 +0000, Diego Villar wrote > Hello, Joern: > > Thanks a lot for your prompt reply. > > *** How did you build the probeAnno object? *** > > I build the ProbeAnno object from a table resembling a pos file, using > the following: > > ProbeAnno<- posToProbeAnno("alt_prom_array.pos", chrNameColumn = > "CHROMOSOME", > probeColumn = "Name", chrPositionColumn = "POSITION", > lengthColumn = "LENGTH", sep="\t", genome="H.Sapiens (hg17)", > microarrayPlatform="Agilent alt prom array (custom)") > > The pos file I used is a tab delimited text file which looks like: > > Name ID CHROMOSOME POSITION COUNT LENGTH > chrX.71280574.71280634 FLJ44635_71280558_16 chrX 71280574 1 60 > chr10.116034763.116034823 VWA2_116034286_477 chr10 116034763 1 60 > chr11.383389.383449 PKP3_383245_144 chr11 383389 1 60 > > I built it this way since the array is an old Agilent custom array > (hg17) and the function that you propose in the Ringo script for > creating a probeAnno object from the genes section of an RG did not > work on my data. > > The probeAnno generated in this way works fine with chipAlongChrom > function on a region of chromosome 11, but after that I get the > mentioned error when using computeRunningMedians. > > chipAlongChrom(eSet, chrom="11", xlim=c(18371851,18373350), > ylim=c(-2,4), probeAnno=ProbeAnno, gff=gff) > > smoothX <- computeRunningMedians(eSet, probeAnno=ProbeAnno, > modColumn = "Cy5", winHalfSize = 400) > > *** Assuming your probeAnno object is called P,what is the output of > validObject(P), str(P["11.start"]) str(P["11.index"])? *** > > > validObject(ProbeAnno) > [1] TRUE > > str(ProbeAnno["11.start"]) > int [1:16314] 186565 186773 186844 186910 189356 189422 189471 > 189516 189604 279308 ... > > str(ProbeAnno["11.index"]) > chr [1:16314] "chr11.186565.186625" "chr11.186773.186833" ... > > *** And please always remember to add the result of typing > "sessionInfo()" in > your R to any question you ask on this list, as this allows us to see > which > software versions you are using *** > > > sessionInfo() > R version 2.9.0 (2009-04-17) > i386-pc-mingw32 > > other attached packages: > [1] Ringo_1.8.0 Matrix_0.999375-24 lattice_0.17-22 limma_2.18.2 > [5] RColorBrewer_1.0-2 Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] annotate_1.22.0 AnnotationDbi_1.6.0 DBI_0.2-4 > [4] genefilter_1.24.0 grid_2.9.0 RSQLite_0.7-1 > [7] splines_2.9.0 survival_2.35-4 tools_2.9.0 > [10] xtable_1.5-5 > > Thanks again for your help, > > Diego > > Con fecha 31/8/2009, "Joern Toedling" <joern.toedling at="" curie.fr=""> > escribi?: > > >Hello, > > > >I'm afraid I do not understand the error message. NAs in your ExpressionSet > >should not be a problem. I suspect that the problem might be with your > >probeAnno object, especially with the probes on chromosome 11 (since it seems > >to work with chromosomes 1 and 10). How did you build the probeAnno object? > >Assuming your probeAnno object is called P, > >what is the output of > >validObject(P) > >str(P["11.start"]) > >str(P["11.index"]) > >? And please always remember to add the result of typing "sessionInfo()" in > >your R to any question you ask on this list, as this allows us to see which > >software versions you are using. > > > >Regards, > >Joern > > > >On Mon, 31 Aug 2009 11:48:17 +0000, Diego Villar wrote > >> Dear All, > >> > >> I am trying to use Ringo for analysis of Agilent platform ChIP- > >> chip. I get the following output/error when applying the computeRunningMedians > >> function to my expression set (2 samples, one normal and one dye- > >> swap): > >> > >> Chromosome 1 ... > >> 170809ds ... 261108no ... > >> Chromosome 10 ... > >> 170809ds ... 261108no ... > >> Chromosome 11 ... > >> 170809ds ... Error en newExprs[chridx, i] <- chrrm : > >> NAs are not allowed in subscribed assignations > >> > >> Does this mean missing values are not allowed at all for this > >> function? How could I modify my input so that the function would > >> work on my data? Would I need to substite NAs somehow in the ExpressionSet? > >> > >> Thanks in advance for your time and help, > >> > >> Diego Villar --- Joern Toedling Institut Curie -- U900 26 rue d'Ulm, 75005 Paris, FRANCE Tel. +33 (0)156246926
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Dear Joern, I looked at the output of the commands you suggested (in some instances only a fragment of the output is copied): table(ProbeAnno["11.unique"]) 0 16314 table(ProbeAnno["11.index"]) chr11.990402.990462 chr11.990469.990529 chr11.990589.990649 1 1 1 chr11.990598.990658 chr11.99098574.99098634 chr11.99098696.99098756 1 1 1 chr11.99191352.99191412 chr11.99191505.99191565 chr11.99191589.99191649 1 1 1 chr11.992384.992444 chr11.992475.992535 chr11.992519.992579 1 1 1 chr11.992572.992632 chr11.992617.992677 chr11.99265506.99265566 1 1 1 chr11.99265661.99265721 chr11.99272465.99272525 chr11.99272618.99272678 1 1 1 chr11.99272726.99272786 chr11.99272763.99272823 chr11.99303967.99304027 1 1 1 chr11.99304052.99304112 chr11.99304124.99304184 chr11.99304202.99304262 1 1 1 chr11.99484048.99484108 chr11.99484323.99484383 chr11.997710.997770 1 1 1 chr11.997821.997881 chr11.997916.997976 chr11.997947.998007 1 1 1 chr11.998012.998072 chr11.998109.998169 chr11.998156.998216 1 1 1 chr11.998214.998274 chr11.998281.998341 chr11.998364.998424 1 1 1 featureNames(eSet) [93143] "chr14.103260174.103260234" "chr15.49420957.49421017" [93145] "chr10.121418721.121418781" "chr3.142475706.142475766" [93147] "chr12.4750441.4750501" "chr19.60858191.60858251" [93149] "chr19.12836986.12837046" "chr2.74610106.74610166" [93151] "chr3.15030218.15030278" "chr4.3302037.3302097" [93153] "chr12.6816461.6816521" "chr16.87787089.87787149" [93155] "chr9.136846349.136846409" "chr14.104905960.104906020" [93157] "chr15.88609844.88609904" "chr19.16097255.16097315" [93159] "chrX.23302155.23302215" "chr22.36928650.36928710" [93161] "chr21.46801174.46801234" "chr1.54802941.54803001" [93163] "chr5.71439940.71440000" "chr13.20109437.20109497" [93165] "chr17.19221465.19221525" "chr15.41265439.41265499" [93167] "chr17.40674754.40674814" "chr9.132028622.132028682" [93169] "chr5.137749901.137749961" "chr2.74916286.74916346" [93171] "chr12.119485201.119485261" "chr1.2021070.2021130" [93173] "chr11.118460384.118460444" "chr9.139292058.139292118" [93175] "chr16.53916013.53916073" "chr14.58726017.58726077" [93177] "chr1.95355225.95355285" "chr20.35407771.35407831" [93179] "chr9.136391391.136391451" "chr17.53678992.53679052" [93181] "chr7.75447663.75447723" "chr3.141175234.141175294" [93183] "chr20.30850078.30850138" "chr17.40681467.40681527" [93185] "chr20.29657541.29657601" "chr7.156895220.156895280" [93187] "chr12.51631466.51631526" "chr19.3086743.3086803" Checking on the error as you indicated I retrieve the following values: smoothX <- computeRunningMedians(eSet, probeAnno=ProbeAnno, + modColumn = "Cy5", winHalfSize = 400) Chromosome 1 ... 170809ds ... 261108no ... Chromosome 10 ... 170809ds ... 261108no ... Chromosome 11 ... 170809ds ... Error en newExprs[chridx, i] <- chrrm : NAs no son permitidos en asignaciones subscritas Enter a frame number, or 0 to exit 1: computeRunningMedians(eSet, probeAnno = ProbeAnno, modColumn = "Cy5", winHa Selecci?n: 1 Called from: eval(expr, envir, enclos) Browse[1]> str(chridx) int [1:16314] 40027 121370 99412 63143 131069 125479 54552 32661 81358 80190 ... Browse[1]> str(i) int 1 Browse[1]> str(chrrm) Named num [1:16314] NA NA NA NA 0.164 ... - attr(*, "names")= chr [1:16314] "186594" "186802" "186874" "186940" ... Thanks, Diego Con fecha 31/8/2009, "Joern Toedling" <joern.toedling at="" curie.fr=""> escribi?: >Well, this looks all fine to me. I cannot tell you immediately where the >problem is, and since I have not run into such an error before, we'll have to >search for the source of the problem together. The fact that chromosomes 1 and >10 work but chromosome 11 does not strongly suggests that there is something >unusual with the elements of that chromosome 11 in the probeAnno object. > >Further things we can check: >table(ProbeAnno["11.unique"]) >table(ProbeAnno["11.index"] %in% featureNames(eSet)) > >Otherwise, consider setting >options(error=recover) >then when the error occurs, type the frame number of'computeRunningMedians' >and please tell me what the result of >str(chridx) >str(i) >str(chrrm) >are. >Alternatively, if you don't mind you could save the objects eSet and ProbeAnno >into a file (using command 'save') and provide them somewhere to me for >downloading. I could check these things myself then. > >Regards, >Joern > > >On Mon, 31 Aug 2009 14:55:41 +0000, Diego Villar wrote >> Hello, Joern: >> >> Thanks a lot for your prompt reply. >> >> *** How did you build the probeAnno object? *** >> >> I build the ProbeAnno object from a table resembling a pos file, using >> the following: >> >> ProbeAnno<- posToProbeAnno("alt_prom_array.pos", chrNameColumn = >> "CHROMOSOME", >> probeColumn = "Name", chrPositionColumn = "POSITION", >> lengthColumn = "LENGTH", sep="\t", genome="H.Sapiens (hg17)", >> microarrayPlatform="Agilent alt prom array (custom)") >> >> The pos file I used is a tab delimited text file which looks like: >> >> Name ID CHROMOSOME POSITION COUNT LENGTH >> chrX.71280574.71280634 FLJ44635_71280558_16 chrX 71280574 1 60 >> chr10.116034763.116034823 VWA2_116034286_477 chr10 116034763 1 60 >> chr11.383389.383449 PKP3_383245_144 chr11 383389 1 60 >> >> I built it this way since the array is an old Agilent custom array >> (hg17) and the function that you propose in the Ringo script for >> creating a probeAnno object from the genes section of an RG did not >> work on my data. >> >> The probeAnno generated in this way works fine with chipAlongChrom >> function on a region of chromosome 11, but after that I get the >> mentioned error when using computeRunningMedians. >> >> chipAlongChrom(eSet, chrom="11", xlim=c(18371851,18373350), >> ylim=c(-2,4), probeAnno=ProbeAnno, gff=gff) >> >> smoothX <- computeRunningMedians(eSet, probeAnno=ProbeAnno, >> modColumn = "Cy5", winHalfSize = 400) >> >> *** Assuming your probeAnno object is called P,what is the output of >> validObject(P), str(P["11.start"]) str(P["11.index"])? *** >> >> > validObject(ProbeAnno) >> [1] TRUE >> > str(ProbeAnno["11.start"]) >> int [1:16314] 186565 186773 186844 186910 189356 189422 189471 >> 189516 189604 279308 ... >> > str(ProbeAnno["11.index"]) >> chr [1:16314] "chr11.186565.186625" "chr11.186773.186833" ... >> >> *** And please always remember to add the result of typing >> "sessionInfo()" in >> your R to any question you ask on this list, as this allows us to see >> which >> software versions you are using *** >> >> > sessionInfo() >> R version 2.9.0 (2009-04-17) >> i386-pc-mingw32 >> >> other attached packages: >> [1] Ringo_1.8.0 Matrix_0.999375-24 lattice_0.17-22 limma_2.18.2 >> [5] RColorBrewer_1.0-2 Biobase_2.4.1 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.22.0 AnnotationDbi_1.6.0 DBI_0.2-4 >> [4] genefilter_1.24.0 grid_2.9.0 RSQLite_0.7-1 >> [7] splines_2.9.0 survival_2.35-4 tools_2.9.0 >> [10] xtable_1.5-5 >> >> Thanks again for your help, >> >> Diego >> >> Con fecha 31/8/2009, "Joern Toedling" <joern.toedling at="" curie.fr=""> >> escribi?: >> >> >Hello, >> > >> >I'm afraid I do not understand the error message. NAs in your ExpressionSet >> >should not be a problem. I suspect that the problem might be with your >> >probeAnno object, especially with the probes on chromosome 11 (since it seems >> >to work with chromosomes 1 and 10). How did you build the probeAnno object? >> >Assuming your probeAnno object is called P, >> >what is the output of >> >validObject(P) >> >str(P["11.start"]) >> >str(P["11.index"]) >> >? And please always remember to add the result of typing "sessionInfo()" in >> >your R to any question you ask on this list, as this allows us to see which >> >software versions you are using. >> > >> >Regards, >> >Joern >> > >> >On Mon, 31 Aug 2009 11:48:17 +0000, Diego Villar wrote >> >> Dear All, >> >> >> >> I am trying to use Ringo for analysis of Agilent platform ChIP- >> >> chip. I get the following output/error when applying the >computeRunningMedians >> >> function to my expression set (2 samples, one normal and one dye- >> >> swap): >> >> >> >> Chromosome 1 ... >> >> 170809ds ... 261108no ... >> >> Chromosome 10 ... >> >> 170809ds ... 261108no ... >> >> Chromosome 11 ... >> >> 170809ds ... Error en newExprs[chridx, i] <- chrrm : >> >> NAs are not allowed in subscribed assignations >> >> >> >> Does this mean missing values are not allowed at all for this >> >> function? How could I modify my input so that the function would >> >> work on my data? Would I need to substite NAs somehow in the ExpressionSet? >> >> >> >> Thanks in advance for your time and help, >> >> >> >> Diego Villar > >--- >Joern Toedling >Institut Curie -- U900 >26 rue d'Ulm, 75005 Paris, FRANCE >Tel. +33 (0)156246926 > Diego Villar Laboratorio 2.5.2 Tel?fono 915854442 Instituto de Investigaciones Biom?dicas "Alberto Sols" CArturo Duperier, 4 28029 Madrid
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