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)> cuffCuffSet 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 [[alternative HTML version deleted]]
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 >[[alternative HTML version deleted]]
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
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
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> PLEASE do read the posting guide
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> and provide commented, minimal, self-contained, reproducible code.
>
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