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Old 12-25-2013, 12:27 PM   #1
nancysky
Junior Member
 
Location: North Carolina

Join Date: Dec 2013
Posts: 2
Default 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
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