DESEQ2 when global gene expression changes exist
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Ron • 0
@39944aa4
Last seen 6 weeks ago
Australia

We performed RNA-seq with cell number normalised ERCC-spike/Loess normalisation in which shows a global shift in gene expression. Is DESEQ2 appropriate to be used in this context to identify DEGs and how would the normalisation be performed?

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DESeq2 • 155 views
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@mikelove
Last seen 8 hours ago
United States

You can specify size factors manually

sizeFactors(dds) <- …

Or use controlGenes argument.

Do either of these before running DESeq()

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