Bioconductor Tcc

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DifferentialExpression Normalization Cancer edgeR baySeq DESeq EBSeq TCC Normalization

updated 11.4 years ago by Koji Kadota ▴ 10 • written 11.4 years ago by Gordon Smyth 53k

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DifferentialExpression Normalization Cancer edgeR baySeq DESeq EBSeq TCC Normalization

updated 11.4 years ago by Jianqiang SUN ▴ 10 • written 11.4 years ago by Pankaj Agarwal ▴ 100

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RNASeq TCC RNASeq TCC

updated 12.1 years ago by Ryan C. Thompson ★ 7.9k • written 12.1 years ago by Guest User ★ 13k

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PROcess Rsamtools Rsubread TCC PROcess Rsamtools Rsubread TCC

13.6 years ago Thomas Girke ★ 1.7k

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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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Answer: Limpa Pipeline Order

A: How barcode-plot enrichment is calculated?

Answer: ROAST compare results with complex design

How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?

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Popular Question to Assa Yeroslaviz ★ 1.5k