Hi Nancy --
cummeRbund is a Bioconductor package so please ask questions about it on the
Bioconductor mailing list.
http://bioconductor.org/help/mailing-list/mailform/
Be sure to include the maintainer packageDescription("cummeRbund")$Maintainer in
the email.
You have the 'latest' version of cummeRbund for R-2.15.3; a more recent version
is available when using R-3.0.2.
Martin
On 01/05/2014 08:12 AM, Yanxiang Shi wrote:
Hi all,
I'm new to RNA-seq analysis. And I'm now trying to use R to visualize the
Galaxy data. I'm using the cummeRbund to deal with the data from cuffdiff
in Galaxy.
Here is the codes I've run:
cuff= readCufflinks (dbFile = "output_database", geneFPKM =
"gene_FPKM_tracking", geneDiff = "gene_differential_expression_testing",
isoformFPKM = "transcript_FPKM_tracking",isoformDiff =
"transcript_differential_expression_testing", TSSFPKM =
"TSS_groups_FPKM_tracking", TSSDiff =
"TSS_groups_differential_expression_testing", CDSFPKM =
"CDS_FPKM_tracking", CDSExpDiff =
"CDS_FPKM_differential_expression_testing", CDSDiff =
"CDS_overloading_diffential_expression_testing", promoterFile =
"promoters_differential_expression_testing", splicingFile =
"splicing_differential_expression_testing", rebuild = T)
cuff
CuffSet instance with:
2 samples
26 genes
44 isoforms
36 TSS
0 CDS
26 promoters
36 splicing
0 relCDS
disp<-dispersionPlot(genes(cuff))
disp
*Error in `$<-.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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