DPA_Timecourse.R encountering an error

[ajritter8]

Hi there,

I'm analyzing a custom human transcriptome and so far all analyses are working except for DPA. For reference, my design is a timecourse with triplicates for 4 timepoints, here's the print out of the factors file data:

h9esc_cyto_jd004 0 1 1
h9esc_cyto_jd005 0 1 1
h9esc_cyto_jd020 0 1 1
h9esc_mono_jd006 1 2 1
h9esc_mono_jd007 1 2 1
h9esc_mono_jd021 1 2 1
h9esc_poll_jd010 2 3 1
h9esc_poll_jd011 2 3 1
h9esc_poll_jd023 2 3 1
h9esc_polh_jd008 3 4 1
h9esc_polh_jd009 3 4 1
h9esc_polh_jd022 3 4 1

Here's the error from the log:

Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
Calls: Favored_tappas ... row.names<- -> row.names<-.data.frame -> .rowNamesDF<-
Execution halted
Differential PolyAdenylation Analysis script ended. Exit value: 1

Which I believe is referring to Line 1321 in the DPA_TimeCourse.R script.
Additionally, I wanted to at least write result_sig, result_predpa and trans_exprs to files so I can piece them together for further analysis myself but updates to DPA_TimeCourse.R don't seem to be affecting re-runs of DPA, even after restarting tappAS and my computer. The Rscripts I've tried changing for troubleshooting are located in .../tappAS/tappas/scripts which I assumed tappAS was calling scripts from but that doesn't seem to be the case.

[almart7]

Dear @ajritter8

Thank you for using tappAS! We are releasing a new version of the tool soon, in which we fix a problem found in this script. Also, are you running the .jar file? You would have to compile the project again for the updates to take effect.

Please try to run the analysis again when the new tappAS version is released and let us know if you are still having problems.