Is my design bad for accounting for Batch Effect in DESEQ2?
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Stephan • 0
@c1dc570b
Last seen 22 months ago
United States

Due to a limited budget, I wasn't able to conduct my experiment in one batch. Instead, I ran the experiment 8 times, twice for each genotype, with each batch containing both a control and treatment condition.

I attempted to add "date" as a variable in the DESEQ formula but ultimately got errors that kept me from including it in the end. I believe the error stemmed from a lack of replication within each batch.

Is it possible to account for a batch effect using this design?

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DESeq2 • 545 views
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@mikelove
Last seen 11 hours ago
United States

You can estimate the treatment effect but you can't estimate the genotype effect, as it is confounded with batch as you've run the experiment.

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