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Answer: Limpa Pipeline Order
by
Gordon Smyth
52k
limpa produces expression quantifications at the protein level, together with observation-level SEs. Although it inputs peptide-level inten…
Comment: Should voomWithQualityWeights still be used when the sample-specific weights var
by
A.Barden
▴ 10
Thanks very much for this informative answer.
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
by
Gordon Smyth
52k
I would recommend now for you to use voomLmFit(), which has all the functionality of voomWithQualityWeights() but with some more features a…
Comment: How to use limma to analyze complex temporal RNAseq data
by
Jinming Cheng
• 0
Hi Jiahao, I generated a dataset to make it similar to yours, and I tried my R codes (`voomLmFit` + `eBayes`) on this dataset, which worke…
Comment: How to use limma to analyze complex temporal RNAseq data
by
Jiahao Tian
• 0
Hi Jinming, I want to make some supplement to my question. The `D` object was built by using `DEGList`, so it is the same as your `y` objec…
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Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: makeChipPackage(): Error in data.frame(..., check.names = FALSE) : arguments
Answer: makeChipPackage(): Error in data.frame(..., check.names = FALSE) : arguments
Answer: Limma : paired samples leading to unexpected estimates
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