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MarioniLab / MNN2017

Code for the MNN manuscript figures
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Cell type labels for the Pancreas datasets #14

Closed ebecht closed 5 years ago

ebecht commented 5 years ago

Hello and thank you for having this public repo! I have run the various scripts in the /Pancreas/ folder as I am interested in studying how batch effects impact DEG methods. However I would like to make sure that I am getting the exact cell type labels you generated (as maybe I have slightly different package versions...). Although most appear to concur I also observed some discrepancies in the heatmap of marker genes for the clusters I obtained.

Therefore, would you mind sharing the *_metadata.tsv tables that are in MNN2017/Pancreas/Data so that I can make sure I have the right cell type labels?

Thank you for your help and efforts!

LTLA commented 5 years ago

I wouldn't worry about it.

Also, I don't know where these files are. Perhaps @MikeDMorgan might still have them, but I gave up trying to maintain the code in this repository. It was easier to make a new repo, as mentioned in the README. That said, the new repo doesn't bother to define cell types for the unannotated data sets; mostly because the clusters (before and after correction) were so clear, it didn't really matter which clustering method you used.

ebecht commented 5 years ago

Ok, I'll go with what I have and double check everything then. Thanks!