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Answer: Ploting of normalized counts after batch removal
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Gordon Smyth
50k
>I am introducing negative values, when I apply limma::removeBatchEffect it doesn't seem correct. That's a misconception. The values input…
Answer: blockwiseModule crashes in the end and doesn't generate modules
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Aslan
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<a href="https://juego-bet.cl/copa-america-2024/">jugabet copa america</a> una plataforma popular de apuestas en línea, ofrece una cobertu…
Comment: Can I trust the differential expression analysis when the two groups overlap on
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BioinfGuru
▴ 30
Did you make any headway? Have you tried plotting a [hierarchical clustering heatmap][1] on tpm normalised count data without any adjustme…
Comment: Ploting of normalized counts after batch removal
by
ATpoint
★ 4.2k
You can use ComBat-seq from the sva package to regress covariates such as the pairing information. Advantage is that it returns "raw correc…
Answer: Ploting of normalized counts after batch removal
by
Michael Love
42k
You can't really plot counts with variance from nuisance covariates removed. I would go the route of using VST data instead (see FAQ).
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Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
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