Hi, when i used CummeRbund to analyze the results of cullmerge output, i successfully built the database with command cuff_data<- readCufflinks(genome='pig',gtfFile='../merged_asm/merged.gtf'). Everything ran well except two errors:
1). fpkmSCVPlot error:
> genes.scv<-fpkmSCVPlot(genes(cuff_data))
Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale.
2). gene feature error:
>myGeneIds<-c('XLOC_000262')
>myGene<-getGenes(cuff_data,myGeneIds)
> myGene
CuffGeneSet instance for 1 genes
Slots:
annotation
fpkm
repFpkm
diff
count
isoforms CuffFeatureSet instance of size 2
TSS CuffFeatureSet instance of size 2
CDS CuffFeatureSet instance of size 1
promoters CuffFeatureSet instance of size 1
splicing CuffFeatureSet instance of size 2
relCDS CuffFeatureSet instance of size 1
>head(features(myGene))> head(features(myGene))
Error in head(features(myGene)) :
error in evaluating the argument 'x' in selecting a method for function 'head': Error in function (classes, fdef, mtable) :
unable to find an inherited method for function ‘features’ for signature ‘"CuffGeneSet"’
Does anyone would like to help?
1). fpkmSCVPlot error:
> genes.scv<-fpkmSCVPlot(genes(cuff_data))
Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale.
2). gene feature error:
>myGeneIds<-c('XLOC_000262')
>myGene<-getGenes(cuff_data,myGeneIds)
> myGene
CuffGeneSet instance for 1 genes
Slots:
annotation
fpkm
repFpkm
diff
count
isoforms CuffFeatureSet instance of size 2
TSS CuffFeatureSet instance of size 2
CDS CuffFeatureSet instance of size 1
promoters CuffFeatureSet instance of size 1
splicing CuffFeatureSet instance of size 2
relCDS CuffFeatureSet instance of size 1
>head(features(myGene))> head(features(myGene))
Error in head(features(myGene)) :
error in evaluating the argument 'x' in selecting a method for function 'head': Error in function (classes, fdef, mtable) :
unable to find an inherited method for function ‘features’ for signature ‘"CuffGeneSet"’
Does anyone would like to help?
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