User: Nicolas Huber

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Posts by Nicolas Huber

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Answer: A: Correcting a nested batch effect
... I think it might not be possible to solve this, even if you had 100 additional control samples. Imagine if the control samples of batch 2 would actually be biologically different from the control samples of batch 1, there is no way to know. If you attempt to remove the 'batch' effect here, you remov ...
written 24 days ago by Nicolas Huber0
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Comment: C: Log2FC data type error in EnhansedVolcano package
... I think you'll have to provide an example, otherwise its impossible to recreate your problem. Just running EnhancedVolcano with numbers like yours does not give this error. ...
written 5 weeks ago by Nicolas Huber0
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Answer: A: Modelling a multiplicative batch effect with DESeq2
... I'm not an expert at all, so here just my thoughts: For a model.matrix if you don't know whether the effect is additive you would write it like this: model.matrix(~ diet + sex + diet:sex) OR model.matrix(~ diet*sex) (took it from http://genomicsclass.github.io/book/pages/expressing_design_formula.ht ...
written 5 weeks ago by Nicolas Huber0
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Comment: C: DESeq2 indirect batch effect removal
... thanks for the answer, I am just not sure I understand it correctly. So the first two code snippets I posted are the correct way to handle this situation with DESeq2? The 2nd question (with the 3rd code snippet) is not about the batch effect, I just observed that results differ when having differen ...
written 6 weeks ago by Nicolas Huber0
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DESeq2 indirect batch effect removal
... Hi, I use DESeq2 in R for differential expression calculation. I already know the design is terrible, but this is what I have to work with ;) Question 1: can I remove the batch effect between 2 groups if their samples do not share a batch, but some of their samples share a batch with a third group? ...
deseq2 batch written 6 weeks ago by Nicolas Huber0 • updated 6 weeks ago by Michael Love26k

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