Samuel Granjeaud

If it helps https://github.com/RGLab/ncdfFlow

Hi, The main part of the CATALYST pipeline aims at importing, clustering and reducing dimensions. The differential analysis is addressed by diffcyt that requires counts, as stated in [section](https://bioconductor.org/packages/release/bioc/vignettes/diffcyt/inst/doc/diffcyt_workflow.html#option-3-individual-functions). diffcyt...

I tested `calcCountsFixed` and it returns the results I attended on 1 example I am working with. I didn't tested the median computations. Thanks @LukaTandaric I think the choice of...

Hello, I think the best way is to use the package in a [step-by-step way](https://bioconductor.org/packages/release/bioc/vignettes/diffcyt/inst/doc/diffcyt_workflow.html#option-3-individual-functions). In the code of generateClusters.R, the few final lines of code show how to add...

I think I mis-read your question. I thought you have carried out a table of counts per sample and per cluster. If the input of the diffcyt wrapper/function is an...

Hi, I am not an expert at modelling, so my opinion is not authoritative. The ids in sample_id are unique, so there is no reason to put this column in...

As I warned you, I am not expert. I answered you in the case it could help. You are right, sample_id is defined in Nowick's article although all values are...

Thanks for your kind message. For sure, it is a pleasure to receive help from you or others. Best regards, Samuel

Hi, The design and contrast matrix are quite generic as diffcyt is calling edgeR. Maybe you would get more audience on [Bioconductor support forum](https://support.bioconductor.org.). Concerning the original question, it's unclear...

It sounds good.