Eduardo Eyras

The transcript IDs from the .ioe file and from the expression file have to match exactly. It looks like they're the same, so I don't understand why it does not...

Hi, please have a look at the SUPPA tutorial in the wiki page https://github.com/comprna/SUPPA/wiki/SUPPA2-tutorial It has some suggestions to visualise the data with the corresponding code. I hope it helps...

Hi, The GTF of the events should be generated, because this is done by the generateEvents operation With no replicates you cannot use the DiffSplice operation, but there may be...

Hi Mary, Thanks for your email. You probably used the "classical" test method? It's certainly unusual to see p-value < 0.05 for zero deltaPSI, but it could be that you...

Thanks Mary, it is surprising that it can give a p-value < 1 with zero delta PSI The empirical method works by testing your observed delta PSI against the distribution...

Thanks a lot for your feedback We have pending looking into this. The calculation is sensitive to missing values, so using -nan may help with some of the problems. As...

Hi, yes, the empirical method is not optimized to sample a constant number of cases with an increasing number of samples. As a consequence, it will attempt to build a...

If we had an optimal way to build the background distribution I would still recommend the empirical method. It is more conservative but more realistic. The classical is fine. You...

Thanks for the suggestion I cc JC and JL, who contributed to the code, in case they can confirm that change E On Thu, 31 Oct 2019 at 21:02, OgnjenMilicevic...

Hello! Very good catch! Avoiding to look for the index twice surely will make a notable performance improvement. I will look into the code, apply the change and test it...