STAGER error: subscript out of bounds

[jma1991]

Hello,

We recently integrated the stageR package into the nf-core/rnasplice workflow. However, a user has reported a technical issue that we're struggling to resolve. When the user sets the alpha parameter in the stageWiseAdjustment function to the standard value of 0.05, they receive a 'subscript out of bounds' error.

Error in `[<-`(`*tmp*`, idCon, 1, value = unlist(txLevelAdjustments)) : 
  subscript out of bounds

Interestingly, adjusting alpha to 1 triggers a different error.

Error in FUN(X[[i]], ...) : 
  Some genes have only one transcript; this is incompatible with DTU correction. Remove these transcripts.

We're seeking guidance on how to address this issue. The user has shared their input files for reference, and the relevant code is located in the run_stager.R script, which you can find in the bin folder of our GitHub repository.

Thanks,
James

[koenvandenberge]

Hi @jma1991

Thank you for reporting. I will take some time to look into this in the coming days.

[SethMagnusJarvis]

I am also having this error. It's when using DRIMSeq though. Someone previously said that it was due to NA values but it would be fixed in the next patch. Is there a quick fix e.g. an easy way to remove NA values so it doesn't throw errors?