Vladimir (Vlad) Kiselev comments

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Vladimir (Vlad) Kiselev

Is there a way to pull out the stability index matrix from the SC3 object?

@yingzhang121 thanks for your question! Please note, that k estimation is not the true k, it is just an estimation, and we also noticed that it overestimates k for UMI-based...

Is there a way to pull out the stability index matrix from the SC3 object?

@yingzhang121 yes, it's a pretty complicated analysis, but I hope you will get good results!

Error in `[.default`(clusts, , paste0("sc3_", hash.table[i, 1], "_clusters"))

Hi, could you please check this issue first? https://github.com/hemberg-lab/SC3/issues/61

Error in `[.default`(clusts, , paste0("sc3_", hash.table[i, 1], "_clusters"))

Hi, sorry for a very long delay, I suppose you figured this out already, or still need help?

Error in `[.default`(clusts, , paste0("sc3_", hash.table[i, 1], "_clusters"))

@reemagit, would you be able to share your dataset so that I can check the errors? You can share it with [email protected]

Error in `[.default`(clusts, , paste0("sc3_", hash.table[i, 1], "_clusters"))

Ok, I will close it for now, thanks for replying.

Error in `[.default`(clusts, , paste0("sc3_", hash.table[i, 1], "_clusters"))

Thanks, Maria! I will try to fix this asap, for the moment please use Maria's advice - have at least two values in `ks`.

No gene names in export results

Hi Daniel, we haven't really changed anything in SC3 in the last ~2 years, so not sure what has happened. Did you manage to solve this problem?

No gene names in export results

Sorry for a late response. Could you check whether you can see gene names when you do `rownames(rowData(sceObj))`? If not then you won't see them in the excel spreadsheet. Please...

Fixed the sparse matrix issue

Thanks, and sorry for a late reply, I will need to test this first and then merge.