Code and documentation/vignette suggestion

[mebbert]

Hi,

Loving Monocle. I have a small suggestion in the code and documentation/vignette. Perhaps I've misunderstood, so correct me if I'm wrong.

I noticed the call to estimate size factors and dispersion is buried at the bottom of a section Converting TPM to mRNA counts that not everyone needs. I skipped that section since I have UMI counts and proceeded with remaining sections, including differential expression. I assumed I had performed any required steps up to that point, and that any other necessary calculations were within the differentialGeneTest call.

My suggestion would be to place the documentation for estimateSizeFactors and estimateDispersions in a more general location. I also think it would be helpful to add a warning or error if someone runs differentialGeneTest without running important steps prior.

Or, have I misunderstood something?

Really appreciate it!

[Xiaojieqiu]

Hi mebbert,

Thanks a lot for your comment, that is right, descriptions about estimateSizeFactors and estimateDispersions should be moved to a more general place. We will update this to our online vignettee soon