Kristoffer Vitting-Seerup

Hi Tobias Thanks for reaching out. Which version of IsoformSwitchAnalyzeR are you using? You can check that via this R command: ``` packageVersion('IsoformSwitchAnalyzeR') ``` If you are not already using...

Just to be sure: Did you re-create the switchAnalyzeRlist (via the `importRdata()` function) with IsoformSwitchAnalyzeR 1.9.3? If not could you try that? If this does not work I would need...

Hi Tobias Sorry for the confusion - you are right that 1.11.3 is the newest version that I wanted you to try with. Do you still get the error? If...

Did you solve this problem Tobias?

Thanks for reaching out. First I will need you to use IsoformSwitchAnalyzeR 1.13.05 which you can obtain either from [Bioconductor](https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html) or [github](https://github.com/kvittingseerup/IsoformSwitchAnalyzeR) as the pfam import have been updated a...

So the pfam results are from the web-server? Did it help update IsoformSwitchAnalyzeR

That sounds stange. Would you be willing to share hte result file so I can fix the problem? Cheers Kristoffer

That would be perfect - thanks!

Hi Fiona Sorry for the late response (holiday). IsoformSwitchAnalyzeR currently does not support data from the ensembldb package directly so it's probably a lot easier to download corresponding GTF file...

Hi fifdick If you use the IsoformSwitchAnalyzeR::importIsoformExpression() to import the Salmon quantification no isoforms are removed. Some isoforms are however missing from the salmon quantification because Salmon automatically removes completely...