Bioconductor PlotDendroAndColors

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wgcna hclust plotdendroandcolors dendrogram

updated 11.0 years ago by James W. MacDonald 68k • written 11.0 years ago by Keith Hughitt ▴ 180

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wgcna plotDendroAndColors Network

updated 11.0 years ago by Peter Langfelder ★ 3.0k • written 11.0 years ago by Keith Hughitt ▴ 180

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Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k

I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…

Comment: Average biological replicates in RNA-seq by boczniak767 ▴ 740

@atpoint Should I first standardise data and then average replicates?

Comment: 3-factor DESeq2 trime-series analysis by gogeni5529 • 0

Thans you @swbarnes2 for the answer. I can see why trying to include all three parameters might be difficult to interpret. But we're inte…

Comment: 3-factor DESeq2 trime-series analysis by swbarnes2 ★ 1.4k

What does your PCA look like? A lot of times, I find that different cell lines are so different from each other, that they should not be d…

Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by yongjie.wang • 0

Thanks for your reply. " normFactors <- exp(-1 * offst(set2)) normFactors <- normFactors / exp(rowMeans(log(normFactors))) normalizat…

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