This is a test version of Biostars. For the public version, visit https://www.biostars.org.
ballgown stattest function error

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

r rna-seq
• 1,453 views • link
updated by Ram Ram • written by fatimarasool135 fatimarasool135

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.
code_formatting

• 0 views • link
written by Ram Ram

0 answers

No answers yet.

Log in to answer this question.

More posts like this