Question: ballgown stattest function error
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gravatar for fatimarasool135
6 months ago by
fatimarasool13540 wrote:

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

rna-seq R • 247 views
ADD COMMENTlink modified 6 months ago by RamRS24k • written 6 months ago by fatimarasool13540
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