User: amckenz

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Posts by amckenz

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Should edgeR-GLM on single cell RNA data be performed on the counts or normalized data?
... I am asking a question relevant to this previous bioconductor-support question: https://support.bioconductor.org/p/71983/ I am wondering: is it better to perform edgeR-GLM on single cell data on the original counts or on normalized data, potentially normalized using scran?  For clarity, below is t ...
edger scran written 18 months ago by amckenz0 • updated 18 months ago by davis90
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Does the normalization pipeline for scran include filtering out genes with low counts?
... I am asking a question about scran, described in this paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0947-7 In the github code, low expression genes were removed prior to running the normalization pipeline in the Zeisel et al. analysis. However, in my reading this did no ...
filtering scran written 18 months ago by amckenz0 • updated 18 months ago by Aaron Lun18k

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