Robert Castelo

The question about what do negative GSVA scores mean has been asked a number of times in the [Bioconductor support site](https://support.bioconductor.org) (see [here](https://support.bioconductor.org/p/9145297), [here](https://support.bioconductor.org/p/84439), [here](https://support.bioconductor.org/p/9142545), [here](https://support.bioconductor.org/p/119709) and [here](https://support.bioconductor.org/p/111171)), which is...

What would you recommend to filter out genes with constant expression (these are often bad for certain calculations because they introduce collinearities, etc.)?

Thanks Henrik for taking the time to share your views on this, I see that the problem is harder than I initially thought. Going back to this specific issue, what...

Thank you so much @ErinBecker and @vlrieg for considering this contribution and for your efforts to integrate it into the episode !! I look forward to seeing it live at...

Yes, I know, a week ago the upstream package Matrix was updated to version 1.5-0, introducing the simultaneous deprecation and defunct of many coercion functions, such as the one that...

I haven't been able to introduce a backward compatibility fix, so I've updated the package to enforce the minimum version of this upstream dependency Matrix to 1.5-0. It should work...

Excellent, thanks!! Two further questions, I've pulled the new image and successfully run: ``` $ docker run mziemann/tallyup ecoli SRR2637695,SRR2637696,SRR2637697,SRR2637698 ``` however, after it finished, there is no file created...

Hi, could you clear up what is the relationship of this problem with GSVA?

I see, thanks Hervé. Looking at the code of the package of GenomicAlignments, the line that builds the `Seqinfo` object [here](https://github.com/Bioconductor/GenomicAlignments/blob/e4021abb60ca7449022cd7a06ee829c02bbfd0cd/R/GAlignments-class.R#L329): ```r seqinfo

hi Hervé, thanks a lot for the thorough analysis of the underlying problem, for the fix, and for starting the feature request on Rsamtools. Indeed, being able to do `genome(gal)