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dkim195 / Ptbp1_Nature_MA

Ptbp1_Nature_MA_Hoang_Kim_et_al_2023
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Clusters missing #1

Closed CountZero-Error closed 3 weeks ago

CountZero-Error commented 1 month ago

Hi, I'm using the data from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE184933 to run your code, but all samples' clusters find is different from the comments in the code, it's missing some of the clusters. For example FACS Cortex, it's missing 14. Doublet and show Oligodendrocyte contamination and 15. Doublet and show Oligodendrocyte contamination. Could u please help me solve this, thank you.

dkim195 commented 1 month ago

Hi, The discrepancies in cluster identification are likely due to differences in R and package versions. I just repeated the step with the same versions and got the same result. Otherwise, those clusters are also easy to find in different package versions, although cluster names might be different.

CountZero-Error commented 1 month ago

Hi, due to some unknown reason I can not install some critical R packages with the version you specified in R 3.6.1. Could you please share with me the outputs for each sample. Much appreciate.