[BioC] Error in dispersionPlot using cummeRbund

Nancy [guest] guest at bioconductor.org
Sun Jan 5 19:07:35 CET 2014

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
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!!!


 -- output of sessionInfo(): 

R version 2.15.3 (2013-03-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)

[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    

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