[R] Error in dispersionPlot using cummeRbund
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. Thank you very much in advance!!! Nancy [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error in dispersionPlot using cummeRbund
Hi Nancy -- cummeRbund is a Bioconductor package so please ask questions about it on the Bioconductor mailing list. http://bioconductor.org/help/mailing-list/mailform/ Be sure to include the maintainer packageDescription(cummeRbund)$Maintainer in the email. You have the 'latest' version of cummeRbund for R-2.15.3; a more recent version is available when using R-3.0.2. Martin On 01/05/2014 08:12 AM, Yanxiang Shi wrote: Hi all, I'm new to RNA-seq analysis. And I'm now trying to use R to visualize the Galaxy data. I'm using the cummeRbund to deal with the data from cuffdiff in Galaxy. Here is the codes I've run: cuff= readCufflinks (dbFile = output_database, geneFPKM = gene_FPKM_tracking, geneDiff = gene_differential_expression_testing, isoformFPKM = transcript_FPKM_tracking,isoformDiff = transcript_differential_expression_testing, TSSFPKM = TSS_groups_FPKM_tracking, TSSDiff = TSS_groups_differential_expression_testing, CDSFPKM = CDS_FPKM_tracking, CDSExpDiff = CDS_FPKM_differential_expression_testing, CDSDiff = CDS_overloading_diffential_expression_testing, promoterFile = promoters_differential_expression_testing, splicingFile = splicing_differential_expression_testing, rebuild = T) cuff CuffSet instance with: 2 samples 26 genes 44 isoforms 36 TSS 0 CDS 26 promoters 36 splicing 0 relCDS disp-dispersionPlot(genes(cuff)) disp *Error in `$-.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. Thank you very much in advance!!! Nancy [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error in dispersionPlot using cummeRbund
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. Thanks, Nancy On Sun, Jan 5, 2014 at 11:12 AM, Yanxiang Shi nancyyx...@gmail.com 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. Thank you very much in advance!!! Nancy [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
