User: chimeric

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chimeric0
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Posts by chimeric

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DESeq2: Is it necessary to include all terms and interactions in LRT tests?
... Hi there, I am wondering if you could comment if I am setting up and interpreting the LRT test correctly.  I am curious if it's necessary to include all terms and interactions, or if I can only include the terms I'm interested in. For example, I have a time course experiment where I have 2 tissue t ...
deseq2 lrt written 2.1 years ago by chimeric0 • updated 2.1 years ago by Gavin Kelly560
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Linear regression in DESeq2
... Is it possible to conduct a linear regression analysis in DESeq2, where one could get a slope, r-squared, and p-value?  Based on this post (https://support.bioconductor.org/p/88254/) it looks like I can get a slope (though it confuses me how log2FoldChange could be interpreted as a slope...clarifica ...
deseq written 2.2 years ago by chimeric0 • updated 2.2 years ago by Michael Love25k
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Comment: C: is it possible to create this comparison?
... Hi hamaor, I think this would still work for you--see the section of the vignette Michael referenced for more info.  To explain, after creating the a "group" factor (dds$treatment and dds$genotype are concatenated to make 1 factor with 4 levels), you can tell the contrasts to run whatever combinati ...
written 3.6 years ago by chimeric0
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Answer: A: is it possible to create this comparison?
... Hi hamaor, I've found the following solution to be the most intuitive way to test whatever combination of factors and levels you're looking for.  The design from this example also looks similar to yours. https://support.bioconductor.org/p/67600/#67612 Cheers, Erin ...
written 3.6 years ago by chimeric0

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