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xihuimeijing / DEGs_Analysis_FDR

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DESeq2 Benchmarking and Normalization #2

Open mingyudu opened 1 year ago

mingyudu commented 1 year ago

Hi,

Hope this message finds you well. I have two questions regarding DESeq2 benchmarking:

Firstly, I'm curious to know if you normalized the raw count data when using DESeq2 as a benchmark. If so, could you please indicate in the code where this was done?

Secondly, based on the code, it seems like you used the single-cell version of DESeq2 instead of the pseudobulk version. Have you tried the pseudobulk approach, and if so, what were your findings?

Thanks, Mingyu

xihuimeijing commented 1 year ago

Hi Mingyu,

Thanks for your questions!

For the first question, we used the raw count matrix as input for DESEeq2 as it expects un-normalized count input.

For the second question, we used the standard bulk version of DESeq2 but not the one for single-cell data.