Error in contrasts<-(tmp, value = contr.funs[1 + isOF[nn]]) : contrasts can be applied only to factors with 2 or more levels
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@fatimarasool135-20519
Last seen 2.4 years ago

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(bgchrXfilt, 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.

Kindly tell me how to resolve it ?

software error ballgown rstudio R stattest • 975 views