Question

Error in dispersionPlot using cummeRbund

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Guest User ★ 13k

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Hi all, I'm new to RNA-seq analysis. And I'm now trying to use R to visualize the Galaxy data. I'm using the cummeRbund to deal with the data from cuffdiff in Galaxy. Here is the codes I've run: > cuff= readCufflinks (dbFile = "output_database", geneFPKM = "gene_FPKM_tracking", geneDiff = "gene_differential_expression_testing", isoformFPKM = "transcript_FPKM_tracking",isoformDiff = "transcript_differential_expression_testing", TSSFPKM = "TSS_groups_FPKM_tracking", TSSDiff = "TSS_groups_differential_expression_testing", CDSFPKM = "CDS_FPKM_tracking", CDSExpDiff = "CDS_FPKM_differential_expression_testing", CDSDiff = "CDS_overloading_diffential_expression_testing", promoterFile = "promoters_differential_expression_testing", splicingFile = "splicing_differential_expression_testing", rebuild = T) > cuff CuffSet instance with: 2 samples 26 genes 44 isoforms 36 TSS 0 CDS 26 promoters 36 splicing 0 relCDS > disp<-dispersionPlot(genes(cuff)) > disp Error in `$<-.data.frame`(`*tmp*`, "SCALE_X", value = 1L) : replacement has 1 rows, data has 0 In addition: Warning message: In max(panels$ROW) : no non-missing arguments to max; returning -Inf Does any one know why there's error? My cummeRbund is the latest version, R is 2.15.3, and cuffdiff v1.3.0. I've tried to search the internet for solutions but apparently it's not a problem that people discussed much. Also, the original files were generated from Galaxy, and the three CDS files were empty. Would that cause the problem? If so, how should I solve it? I used reference sequence as the fasta file, and the gtf annotation file from Ensembl. Thank you very much in advance!!! Nancy -- output of sessionInfo(): R version 2.15.3 (2013-03-01) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] splines grid stats graphics grDevices utils datasets methods base other attached packages: [1] edgeR_3.0.8 limma_3.14.4 affycoretools_1.30.0 KEGG.db_2.8.0 [5] GO.db_2.8.0 AnnotationDbi_1.20.7 WGCNA_1.34 Hmisc_3.13-0 [9] Formula_1.1-1 survival_2.37-2 lattice_0.20-13 cluster_1.14.3 [13] flashClust_1.01-2 dynamicTreeCut_1.60-1 plyr_1.8 affy_1.36.1 [17] Biobase_2.18.0 cummeRbund_2.0.0 Gviz_1.2.1 rtracklayer_1.18.2 [21] GenomicRanges_1.10.7 IRanges_1.16.6 fastcluster_1.1.13 reshape2_1.2.2 [25] ggplot2_0.9.3.1 RSQLite_0.11.4 DBI_0.2-7 BiocGenerics_0.4.0 [29] BiocInstaller_1.8.3 loaded via a namespace (and not attached): [1] affyio_1.26.0 annaffy_1.30.0 annotate_1.36.0 AnnotationForge_1.0.3 [5] biomaRt_2.14.0 Biostrings_2.26.3 biovizBase_1.6.2 bitops_1.0-5 [9] BSgenome_1.26.1 Category_2.24.0 codetools_0.2-8 colorspace_1.2-4 [13] dichromat_2.0-0 digest_0.6.4 doParallel_1.0.6 foreach_1.4.1 [17] gcrma_2.30.0 gdata_2.13.2 genefilter_1.40.0 GenomicFeatures_1.10.2 [21] GOstats_2.24.0 gplots_2.11.0 graph_1.36.2 GSEABase_1.20.2 [25] gtable_0.1.2 gtools_2.7.0 impute_1.32.0 iterators_1.0.6 [29] labeling_0.2 MASS_7.3-23 matrixStats_0.8.12 munsell_0.4.2 [33] parallel_2.15.3 preprocessCore_1.20.0 proto_0.3-10 R.methodsS3_1.5.2 [37] RBGL_1.34.0 RColorBrewer_1.0-5 RCurl_1.95-4.1 reshape_0.8.4 [41] Rsamtools_1.10.2 scales_0.2.3 stats4_2.15.3 stringr_0.6.2 [45] tools_2.15.3 XML_3.95-0.2 xtable_1.7-1 zlibbioc_1.4.0 -- Sent via the guest posting facility at bioconductor.org.

GO cummeRbund GO cummeRbund • 2.0k views

ADD COMMENT • link updated 10.9 years ago by Loyal Goff ▴ 140 • written 10.9 years ago by Guest User ★ 13k

score 0 · Answer 1 · 2014-01-06

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Loyal Goff ▴ 140

@loyal-goff-4989

Last seen 10.2 years ago

Hi Nancy, I am fairly certain that the problem is that you are using a very old version of cufflinks (cuffdiff). There have been a good amount of changes since as recent as v2.0, and it is highly recommended that all users upgrade to the most recent version. In particular for your case, the ?dispersionPlot()? function relies on data that was not emitted from cuffdiff prior to v2.0. I?m not really sure what the current version of cufflinks is on Galaxy but if you have the option of using 2.1.1 it is most highly recommended. Especially if you would like to take full advantage of the cummerbund package as well. Cheers, Loyal On Jan 5, 2014, at 1:07 PM, Nancy [guest] <guest at="" bioconductor.org=""> wrote: > > Hi all, > > I'm new to RNA-seq analysis. And I'm now trying to use R to visualize the Galaxy data. I'm using the cummeRbund to deal with the data from cuffdiff in Galaxy. > > Here is the codes I've run: > >> cuff= readCufflinks (dbFile = "output_database", geneFPKM = "gene_FPKM_tracking", geneDiff = "gene_differential_expression_testing", isoformFPKM = "transcript_FPKM_tracking",isoformDiff = "transcript_differential_expression_testing", TSSFPKM = "TSS_groups_FPKM_tracking", TSSDiff = "TSS_groups_differential_expression_testing", CDSFPKM = "CDS_FPKM_tracking", CDSExpDiff = "CDS_FPKM_differential_expression_testing", CDSDiff = "CDS_overloading_diffential_expression_testing", promoterFile = "promoters_differential_expression_testing", splicingFile = "splicing_differential_expression_testing", rebuild = T) > >> cuff > CuffSet instance with: > 2 samples > 26 genes > 44 isoforms > 36 TSS > 0 CDS > 26 promoters > 36 splicing > 0 relCDS > >> disp<-dispersionPlot(genes(cuff)) >> disp > Error in `$<-.data.frame`(`*tmp*`, "SCALE_X", value = 1L) : > replacement has 1 rows, data has 0 > In addition: Warning message: > In max(panels$ROW) : no non-missing arguments to max; returning -Inf > > Does any one know why there's error? My cummeRbund is the latest version, R is 2.15.3, and cuffdiff v1.3.0. > > I've tried to search the internet for solutions but apparently it's not a problem that people discussed much. > > Also, the original files were generated from Galaxy, and the three CDS files were empty. Would that cause the problem? If so, how should I solve it? I used reference sequence as the fasta file, and the gtf annotation file from Ensembl. > > Thank you very much in advance!!! > > Nancy > > -- output of sessionInfo(): > > R version 2.15.3 (2013-03-01) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] splines grid stats graphics grDevices utils datasets methods base > > other attached packages: > [1] edgeR_3.0.8 limma_3.14.4 affycoretools_1.30.0 KEGG.db_2.8.0 > [5] GO.db_2.8.0 AnnotationDbi_1.20.7 WGCNA_1.34 Hmisc_3.13-0 > [9] Formula_1.1-1 survival_2.37-2 lattice_0.20-13 cluster_1.14.3 > [13] flashClust_1.01-2 dynamicTreeCut_1.60-1 plyr_1.8 affy_1.36.1 > [17] Biobase_2.18.0 cummeRbund_2.0.0 Gviz_1.2.1 rtracklayer_1.18.2 > [21] GenomicRanges_1.10.7 IRanges_1.16.6 fastcluster_1.1.13 reshape2_1.2.2 > [25] ggplot2_0.9.3.1 RSQLite_0.11.4 DBI_0.2-7 BiocGenerics_0.4.0 > [29] BiocInstaller_1.8.3 > > loaded via a namespace (and not attached): > [1] affyio_1.26.0 annaffy_1.30.0 annotate_1.36.0 AnnotationForge_1.0.3 > [5] biomaRt_2.14.0 Biostrings_2.26.3 biovizBase_1.6.2 bitops_1.0-5 > [9] BSgenome_1.26.1 Category_2.24.0 codetools_0.2-8 colorspace_1.2-4 > [13] dichromat_2.0-0 digest_0.6.4 doParallel_1.0.6 foreach_1.4.1 > [17] gcrma_2.30.0 gdata_2.13.2 genefilter_1.40.0 GenomicFeatures_1.10.2 > [21] GOstats_2.24.0 gplots_2.11.0 graph_1.36.2 GSEABase_1.20.2 > [25] gtable_0.1.2 gtools_2.7.0 impute_1.32.0 iterators_1.0.6 > [29] labeling_0.2 MASS_7.3-23 matrixStats_0.8.12 munsell_0.4.2 > [33] parallel_2.15.3 preprocessCore_1.20.0 proto_0.3-10 R.methodsS3_1.5.2 > [37] RBGL_1.34.0 RColorBrewer_1.0-5 RCurl_1.95-4.1 reshape_0.8.4 > [41] Rsamtools_1.10.2 scales_0.2.3 stats4_2.15.3 stringr_0.6.2 > [45] tools_2.15.3 XML_3.95-0.2 xtable_1.7-1 zlibbioc_1.4.0 > > -- > Sent via the guest posting facility at bioconductor.org.

ADD COMMENT • link 10.9 years ago Loyal Goff ▴ 140

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Hi Loyal, Thank you very much for the answer (for some reason it went to my spam so I just got to see it....)! I was using the server from my university which has only one version of the cufflinks. The https://usegalaxy.org/ is a free platform, right? I will try my data there then. Thanks, Nancy On Mon, Jan 6, 2014 at 1:09 PM, Loyal A. Goff <lgoff@csail.mit.edu> wrote: > Hi Nancy, > I am fairly certain that the problem is that you are using a very old > version of cufflinks (cuffdiff). There have been a good amount of changes > since as recent as v2.0, and it is highly recommended that all users > upgrade to the most recent version. In particular for your case, the > dispersionPlot() function relies on data that was not emitted from > cuffdiff prior to v2.0. Im not really sure what the current version of > cufflinks is on Galaxy but if you have the option of using 2.1.1 it is most > highly recommended. Especially if you would like to take full advantage of > the cummerbund package as well. > > > Cheers, > Loyal > > > On Jan 5, 2014, at 1:07 PM, Nancy [guest] <guest@bioconductor.org> wrote: > > > > > Hi all, > > > > I'm new to RNA-seq analysis. And I'm now trying to use R to visualize > the Galaxy data. I'm using the cummeRbund to deal with the data from > cuffdiff in Galaxy. > > > > Here is the codes I've run: > > > >> cuff= readCufflinks (dbFile = "output_database", geneFPKM = > "gene_FPKM_tracking", geneDiff = "gene_differential_expression_testing", > isoformFPKM = "transcript_FPKM_tracking",isoformDiff = > "transcript_differential_expression_testing", TSSFPKM = > "TSS_groups_FPKM_tracking", TSSDiff = > "TSS_groups_differential_expression_testing", CDSFPKM = > "CDS_FPKM_tracking", CDSExpDiff = > "CDS_FPKM_differential_expression_testing", CDSDiff = > "CDS_overloading_diffential_expression_testing", promoterFile = > "promoters_differential_expression_testing", splicingFile = > "splicing_differential_expression_testing", rebuild = T) > > > >> cuff > > CuffSet instance with: > > 2 samples > > 26 genes > > 44 isoforms > > 36 TSS > > 0 CDS > > 26 promoters > > 36 splicing > > 0 relCDS > > > >> disp<-dispersionPlot(genes(cuff)) > >> disp > > Error in `$<-.data.frame`(`*tmp*`, "SCALE_X", value = 1L) : > > replacement has 1 rows, data has 0 > > In addition: Warning message: > > In max(panels$ROW) : no non-missing arguments to max; returning -Inf > > > > Does any one know why there's error? My cummeRbund is the latest > version, R is 2.15.3, and cuffdiff v1.3.0. > > > > I've tried to search the internet for solutions but apparently it's not > a problem that people discussed much. > > > > Also, the original files were generated from Galaxy, and the three CDS > files were empty. Would that cause the problem? If so, how should I solve > it? I used reference sequence as the fasta file, and the gtf annotation > file from Ensembl. > > > > Thank you very much in advance!!! > > > > Nancy > > > > -- output of sessionInfo(): > > > > R version 2.15.3 (2013-03-01) > > Platform: x86_64-w64-mingw32/x64 (64-bit) > > > > locale: > > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 > > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > > [5] LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] splines grid stats graphics grDevices utils datasets > methods base > > > > other attached packages: > > [1] edgeR_3.0.8 limma_3.14.4 affycoretools_1.30.0 > KEGG.db_2.8.0 > > [5] GO.db_2.8.0 AnnotationDbi_1.20.7 WGCNA_1.34 > Hmisc_3.13-0 > > [9] Formula_1.1-1 survival_2.37-2 lattice_0.20-13 > cluster_1.14.3 > > [13] flashClust_1.01-2 dynamicTreeCut_1.60-1 plyr_1.8 > affy_1.36.1 > > [17] Biobase_2.18.0 cummeRbund_2.0.0 Gviz_1.2.1 > rtracklayer_1.18.2 > > [21] GenomicRanges_1.10.7 IRanges_1.16.6 fastcluster_1.1.13 > reshape2_1.2.2 > > [25] ggplot2_0.9.3.1 RSQLite_0.11.4 DBI_0.2-7 > BiocGenerics_0.4.0 > > [29] BiocInstaller_1.8.3 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.26.0 annaffy_1.30.0 annotate_1.36.0 > AnnotationForge_1.0.3 > > [5] biomaRt_2.14.0 Biostrings_2.26.3 biovizBase_1.6.2 > bitops_1.0-5 > > [9] BSgenome_1.26.1 Category_2.24.0 codetools_0.2-8 > colorspace_1.2-4 > > [13] dichromat_2.0-0 digest_0.6.4 doParallel_1.0.6 > foreach_1.4.1 > > [17] gcrma_2.30.0 gdata_2.13.2 genefilter_1.40.0 > GenomicFeatures_1.10.2 > > [21] GOstats_2.24.0 gplots_2.11.0 graph_1.36.2 > GSEABase_1.20.2 > > [25] gtable_0.1.2 gtools_2.7.0 impute_1.32.0 > iterators_1.0.6 > > [29] labeling_0.2 MASS_7.3-23 matrixStats_0.8.12 > munsell_0.4.2 > > [33] parallel_2.15.3 preprocessCore_1.20.0 proto_0.3-10 > R.methodsS3_1.5.2 > > [37] RBGL_1.34.0 RColorBrewer_1.0-5 RCurl_1.95-4.1 > reshape_0.8.4 > > [41] Rsamtools_1.10.2 scales_0.2.3 stats4_2.15.3 > stringr_0.6.2 > > [45] tools_2.15.3 XML_3.95-0.2 xtable_1.7-1 > zlibbioc_1.4.0 > > > > -- > > Sent via the guest posting facility at bioconductor.org. > > [[alternative HTML version deleted]]

ADD REPLY • link 10.9 years ago Yanxiang Shi ▴ 40

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I rerun my data on usegalaxy.org again starting from my Tophat2 results, using the gtf file with p_id. In fact my gtf file from Ensembl doesn't have p_id. I manually changed the protein_id into p_id. Once again, this time no p_id was seen in the cuffmerge data. I feel really frustrated. What may be the problem? Any suggestion is welcome!!! Thanks!!! Nancy On Fri, Jan 10, 2014 at 10:28 PM, Yanxiang Shi <nancyyxshi@gmail.com> wrote: > Hi Loyal, > > Thank you very much for the answer (for some reason it went to my spam so > I just got to see it....)! I was using the server from my university which > has only one version of the cufflinks. The https://usegalaxy.org/ is a > free platform, right? I will try my data there then. > > Thanks, > Nancy > > > > On Mon, Jan 6, 2014 at 1:09 PM, Loyal A. Goff <lgoff@csail.mit.edu> wrote: > >> Hi Nancy, >> I am fairly certain that the problem is that you are using a very old >> version of cufflinks (cuffdiff). There have been a good amount of changes >> since as recent as v2.0, and it is highly recommended that all users >> upgrade to the most recent version. In particular for your case, the >> dispersionPlot() function relies on data that was not emitted from >> cuffdiff prior to v2.0. Im not really sure what the current version of >> cufflinks is on Galaxy but if you have the option of using 2.1.1 it is most >> highly recommended. Especially if you would like to take full advantage of >> the cummerbund package as well. >> >> >> Cheers, >> Loyal >> >> >> On Jan 5, 2014, at 1:07 PM, Nancy [guest] <guest@bioconductor.org> wrote: >> >> > >> > Hi all, >> > >> > I'm new to RNA-seq analysis. And I'm now trying to use R to visualize >> the Galaxy data. I'm using the cummeRbund to deal with the data from >> cuffdiff in Galaxy. >> > >> > Here is the codes I've run: >> > >> >> cuff= readCufflinks (dbFile = "output_database", geneFPKM = >> "gene_FPKM_tracking", geneDiff = "gene_differential_expression_testing", >> isoformFPKM = "transcript_FPKM_tracking",isoformDiff = >> "transcript_differential_expression_testing", TSSFPKM = >> "TSS_groups_FPKM_tracking", TSSDiff = >> "TSS_groups_differential_expression_testing", CDSFPKM = >> "CDS_FPKM_tracking", CDSExpDiff = >> "CDS_FPKM_differential_expression_testing", CDSDiff = >> "CDS_overloading_diffential_expression_testing", promoterFile = >> "promoters_differential_expression_testing", splicingFile = >> "splicing_differential_expression_testing", rebuild = T) >> > >> >> cuff >> > CuffSet instance with: >> > 2 samples >> > 26 genes >> > 44 isoforms >> > 36 TSS >> > 0 CDS >> > 26 promoters >> > 36 splicing >> > 0 relCDS >> > >> >> disp<-dispersionPlot(genes(cuff)) >> >> disp >> > Error in `$<-.data.frame`(`*tmp*`, "SCALE_X", value = 1L) : >> > replacement has 1 rows, data has 0 >> > In addition: Warning message: >> > In max(panels$ROW) : no non-missing arguments to max; returning -Inf >> > >> > Does any one know why there's error? My cummeRbund is the latest >> version, R is 2.15.3, and cuffdiff v1.3.0. >> > >> > I've tried to search the internet for solutions but apparently it's not >> a problem that people discussed much. >> > >> > Also, the original files were generated from Galaxy, and the three CDS >> files were empty. Would that cause the problem? If so, how should I solve >> it? I used reference sequence as the fasta file, and the gtf annotation >> file from Ensembl. >> > >> > Thank you very much in advance!!! >> > >> > Nancy >> > >> > -- output of sessionInfo(): >> > >> > R version 2.15.3 (2013-03-01) >> > Platform: x86_64-w64-mingw32/x64 (64-bit) >> > >> > locale: >> > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> States.1252 >> > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C >> > [5] LC_TIME=English_United States.1252 >> > >> > attached base packages: >> > [1] splines grid stats graphics grDevices utils >> datasets methods base >> > >> > other attached packages: >> > [1] edgeR_3.0.8 limma_3.14.4 affycoretools_1.30.0 >> KEGG.db_2.8.0 >> > [5] GO.db_2.8.0 AnnotationDbi_1.20.7 WGCNA_1.34 >> Hmisc_3.13-0 >> > [9] Formula_1.1-1 survival_2.37-2 lattice_0.20-13 >> cluster_1.14.3 >> > [13] flashClust_1.01-2 dynamicTreeCut_1.60-1 plyr_1.8 >> affy_1.36.1 >> > [17] Biobase_2.18.0 cummeRbund_2.0.0 Gviz_1.2.1 >> rtracklayer_1.18.2 >> > [21] GenomicRanges_1.10.7 IRanges_1.16.6 fastcluster_1.1.13 >> reshape2_1.2.2 >> > [25] ggplot2_0.9.3.1 RSQLite_0.11.4 DBI_0.2-7 >> BiocGenerics_0.4.0 >> > [29] BiocInstaller_1.8.3 >> > >> > loaded via a namespace (and not attached): >> > [1] affyio_1.26.0 annaffy_1.30.0 annotate_1.36.0 >> AnnotationForge_1.0.3 >> > [5] biomaRt_2.14.0 Biostrings_2.26.3 biovizBase_1.6.2 >> bitops_1.0-5 >> > [9] BSgenome_1.26.1 Category_2.24.0 codetools_0.2-8 >> colorspace_1.2-4 >> > [13] dichromat_2.0-0 digest_0.6.4 doParallel_1.0.6 >> foreach_1.4.1 >> > [17] gcrma_2.30.0 gdata_2.13.2 genefilter_1.40.0 >> GenomicFeatures_1.10.2 >> > [21] GOstats_2.24.0 gplots_2.11.0 graph_1.36.2 >> GSEABase_1.20.2 >> > [25] gtable_0.1.2 gtools_2.7.0 impute_1.32.0 >> iterators_1.0.6 >> > [29] labeling_0.2 MASS_7.3-23 matrixStats_0.8.12 >> munsell_0.4.2 >> > [33] parallel_2.15.3 preprocessCore_1.20.0 proto_0.3-10 >> R.methodsS3_1.5.2 >> > [37] RBGL_1.34.0 RColorBrewer_1.0-5 RCurl_1.95-4.1 >> reshape_0.8.4 >> > [41] Rsamtools_1.10.2 scales_0.2.3 stats4_2.15.3 >> stringr_0.6.2 >> > [45] tools_2.15.3 XML_3.95-0.2 xtable_1.7-1 >> zlibbioc_1.4.0 >> > >> > -- >> > Sent via the guest posting facility at bioconductor.org. >> >> [[alternative HTML version deleted]]

ADD REPLY • link 10.9 years ago Yanxiang Shi ▴ 40