Differential expression analysis using SCAN data

Question

[Stikos]

Hi all,

I'd like to identify differentially expressed genes between various pairs of groups and the gene expression data I have avaialble have been SCAN normalized. To my understanding, I cannot use popular tools such as DESeq2. Is there any method that can be reliably applied or should I have the read count data for such process?

Thanks in advance!

[ATpoint]

I do not know the package you mention (SCAN) and I have never seen it being references in any paper. That does not mean it is not a good method (as said I do not know the method), but if you have the raw read counts available then I'd use these. That makes it simple to follow standard protocols as described in the manuals of e.g. DESeq2 or edgeR so methods that are established and have a large userbase. If you must use SCAN, and it produces results on the log scale maybe you can tackle it via the methods implemented in limma.