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Reasons for extremely low number of DESeq identified differentially expressed genes after RNAseq?

The reason is that, according to your PCA, your treatment doesn't do very much. It's not what you want to hear, but that's probably the truth. You probably didn't do anything wrong, it's just what ...
swbarnes2's user avatar
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Reasons for extremely low number of DESeq identified differentially expressed genes after RNAseq?

Generally, the recommended way of doing such analysis is exploring data by a dimensionality reduction technique such as PCA, e.g. implemented in DESeq2 via plotPCA. ...
ATpoint's user avatar
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time*treatment series with repeated (i.e: NOT independent) sampling of replicates

Partial answer: because your replicates involved a physical splitting of the input, I would consider them to be sufficiently distinct to be considered biological replicates. EdgeR should consider ...
gringer's user avatar
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