Eduardo Eyras

hi, sorry for the delayed reply. It is a standard lm() function, correcting with co-variables. We used those that we observed had the strongest confounding effect. It is a fairly...

Hi, Yes, multiple test correction (MTC) adjust the p-value for the fact that your tests are not completely independent of each other. rMATS corrects per event type because you have...

Not yet. For that number of samples, the classical test is still recommended. Thanks. E.

Hi, Are you using a clone from the github repository? I checked the code and the nan_th parameter should be passed into the function, also for the classical method. E....

Could you please try with the code in github? Thanks Eduardo On Fri, 6 Oct 2023 at 00:15, vsarsam ***@***.***> wrote: > Hey, > thanks for the quick response :)...

Have you tried the --method classical? The empirical is not as efficient. E On Wed, 7 Jun 2023 at 21:30, sarahhp ***@***.***> wrote: > I'm getting the same dpsi.temp.0 output...

Do you have many NA's? You can control how many are accepted. Or perhaps you're using other symbol for NA's? Thanks E. On Fri, 9 Jun 2023 at 21:01, sarahhp...

Are you using the code installed from conda, or downloaded from the repository? We did fix the handling of the -nan parameter a while back. Also, which test are you...

Thanks Could you please send me sample input files and your command line. I can try to reproduce the problem Thanks E. On Sat, 19 Aug 2023 at 00:57, sarahhp...

Hello, it would be better to use one single GTF file, so that you can compare events across conditions. You will also need an expression file for each sample based...