DESeq2 remove batch effect
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zxc741xb • 0
@36e3087a
Last seen 10 months ago
Taiwan

Hi, I'm new in biological analysis.

I want to use DESeq2 to do my analysis, I have batch 1 and batch 2, and the batch equals group.

My colData

If I want to remove the batch effect, should I only use design = ~ group + condition, or I should use design = ~ batch + group + condition ?

And this is PCA result, is there any batch effect exist? Should I remove batch effect before WGCNA? enter image description here

BatchEffect RNASeqData WGCNA DESeq2 • 1.2k views
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DESeq2 remove batch effect is always my favorite and finally I got the detail here to know how to do it. To get the Brisbane Tree Removal we can find the best services that are good to provide us the best services for tree removal.

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@james-w-macdonald-5106
Last seen 5 hours ago
United States

You can use either group or batch (if you ensure it's a factor first), but not both. For WGCNA you should convert from counts using one of the methods in this section of the vignette.. You may also want to remove the batch effect after that (or maybe you can use blind = TRUE if the design is just ~ group. But WGCNA isn't a Bioconductor package, so this isn't really the place to get help for that package.

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Thank you, so the process is

  1. Remove batch effect (using combat)
  2. Vst convert
  3. WGCNA

Right?

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I would reverse 1 and 2

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Re: geometry dash online

And then?

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