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Published 20 hours ago • verified publisher icon AntonioDeFalco

Normalization?

Open DGladish opened this issue 1 year ago • 2 comments

Hi!

Just wanted to see if the read counts have to be normalized to account for sequencing depth, or if unnormalized counts are used as input.

Thank you!

DGladish avatar Nov 16 '23 01:11 DGladish

Hi @DGladish, Non-normalized counts are used as input since SCEVAN analyses each sample individually and does not take this normalization into account even in the multi-sample analysis, each sample is processed and then the output is compared. We recommend this type of use, do you need to analyze a merged matrix of different sequencing?

Thanks, Regards.

AntonioDeFalco avatar Nov 22 '23 11:11 AntonioDeFalco

Nope! I am working on 4 separate samples (cancer scRNA-seq data at diagnosis & relapse, + 2 healthy donors). Thank you for the clarification!

Another question, does SCEVAN work if the input is a data frame? Or does the data type have to be matrix?

DGladish avatar Nov 22 '23 23:11 DGladish