cummeRbund 'features' error

[shengzizhang]

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?

[apadr007]

same

I'm having the same problem

> head(fpkm(myGenes))
Error in head(fpkm(myGenes)) :
error in evaluating the argument 'x' in selecting a method for function 'head': Error in myFPKM$conf_hi - myFPKM$fpkm :
non-numeric argument to binary operator


Anyone have an idea?

[moredd]

I also had the error #1 in CummeRbund, although for all other graphs it worked well...
I've tried a lot of possibilities, as genes.scv<-fpkmSCVPlot(genes(cuff),c(1)) (and variations like c(2), c(10), etc)

Moreover, I tried
> genes.scv<-fpkmSCVPlot(genes(cuff_data))
Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale.
>c(1)
>[1] 1
>1
Then > [1] 1 appears again....

Anyone could help?