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Hi Michael,
I have a question for data preprocessing before sending them out for clustering: I think we directly compute the distance on original data without doing PCA to reduce its dimensions, will this affect the results of clustering, especially for distance measurements like Euclidean distance and cosine similarity?

Hi,

Thanks for depositing your code and the dismay package.

During calculating the co-expression matrices, raw umi counts was used as input, as apposed to the umi counts normalized to per cell or log(normalized umi). This is somehow different than what people would do in the bulk RNA-Seq area, where log(normCounts) are usually used. Would you worry that the co-expression metrics will be affected by using raw umi counts, which are apparently not normally distributed? Or am I missing something here?

Thanks a lot.