Does software significantly impact fold change values?
I am using STAR to map reads and then I am using DESeq2 to make differential analysis. Originally this was made with Cufflinks and there were 308 differentially expressed genes - I have 0 because the fold change values are lower than 2. It is possible the software makes such a change or it could be other mistakes?
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Jeremy Leipzig
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margarett •
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margarett •
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Yes there is the lfc shrinkage feature of DESeq2 which will reduce your fold changes, especially when you don't have many replicates https://www.biostars.org/post/search/?query=shrinkage+deseq2
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