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deseq2 contrast synergy

updated 10 months ago by Jane ▴ 10 • written 4.9 years ago by steven wink ▴ 90

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contrast edgeR DESeq2

updated 10 months ago by James W. MacDonald 65k • written 10 months ago by Cristina • 0

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DESeq2 contrast DifferentialExpression

6 weeks ago • updated 5 weeks ago Chanderkant Chaudhary • 0

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Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0

Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …

Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k

Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…

Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k

Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…

Answer: Why does GSEA on edgeR results for randomized samples give highly significant p- by Gordon Smyth 50k

You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …

Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k

In that case both time and treatment are identical things, so choose one and go with it.

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Bioconductor 3.19 is Released!

Bioconductor 3.19 is Released!

Answer: DEseq2 coefficient

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