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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…

Answer: DESeq2 used with zinbwave weights - Differences on contrasts calculations by Michael Love 43k

There is one case where it is different in the code (it's here in the forum but probably buried under thousands of posts). If you have a mu…

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