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 <nancyyxshi@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
>

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