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.  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@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.
>
>

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