User: hoe

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hoe0
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Comment: C: differentially expressed genes without contrasts
... I think my answer can be found in chapter 9 (2016 edition) on p.40-41. For a fixed reference group, there is no need to construct a contrast.matrix because eBayes and topTable always use 'intercept' or coef=1 as the reference for comparison. For this scenario, design <- model.matrix(~conditions). ...
written 2.3 years ago by hoe0
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differentially expressed genes without contrasts
... Hi I'm confused about how to identify differentially expressed genes (DEGs) in a single-channel expt. Is it possible to identify DEGs without making a contrast.matrix? I saw examples just did: fit <- lmFit(...) fit <- eBayes(fit) tt <- topTable(fit, coef=2) All DEGs are stored in tt ...
limma toptable makecontrasts contrast matrix written 2.3 years ago by hoe0 • updated 2.3 years ago by Ryan C. Thompson7.4k

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