Entering edit mode
5.0 years ago
fatimarasool135
▴
90
Hi,
I have encountered an error while running the stattest function of ballgown
I have run the command as
> results_transcripts = stattest(bg_chrX_filt,feature= c("gene","exon","intron","transcript"),covariate="part", getFC=TRUE,meas="FPKM", timecourse = FALSE, df=2)
The error was
Error in contrasts<-(*tmp*, value = contr.funs[1 + isOF[nn]]) :
contrasts can be applied only to factors with 2 or more levels
Again I modified the above command. The command is
> results_transcripts = stattest(bg_chrX_filt,feature= c("gene","exon","intron","transcript"),covariate="part", getFC=TRUE,meas="FPKM", timecourse = TRUE)
The error was
Error in contrasts<-(*tmp*, value = contr.funs[1 + isOF[nn]]) :
contrasts can be applied only to factors with 2 or more levels
In addition: Warning message:
In stattest(bg_chrX_filt, feature = c("gene", "exon", "intron", :
Not enough timepoints (or values of covariate) to fit a spline model with 4 degrees of freedom. Statistical tests will be run treating time as categorical. You can also re-run the analysis with decreased df.
Please tell me how to resolve these error