[BioC] Error in dispersionPlot using cummeRbund

[Loyal A. Goff]

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.