Bioconductor Topaseq

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ToPASeq Deprecation

2.6 years ago pgauthi1 • 0

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842

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topaseq

updated 6.4 years ago by Gordon Smyth 51k • written 6.4 years ago by Aditya Saxena ▴ 10

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1.1k

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ToPASeq SPIA pathway analysis R

6.6 years ago fawazfebin ▴ 60

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1.1k

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topaseq

updated 7.1 years ago by Martin Morgan 25k • written 7.1 years ago by Aditya Saxena ▴ 10

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1.8k

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installation package installation topaseq igraph LD_LIBRARY_PATH

7.8 years ago jan.soderman • 0

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990

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ToPASeq

updated 7.9 years ago by theobroma22 ▴ 10 • written 7.9 years ago by rubi ▴ 110

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rnaseq Topaseq

8.6 years ago saamar.rajput • 0

7 results • Page 1 of 1

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Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k

I'm adding my comment to the threaded section ... I don't have any suggestions here but whatever method you're using is not appropriate up…

Comment: ANOVA like approach of edgeR by Yunshun Chen ▴ 880

If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …

Comment: ANOVA like approach of edgeR by SamGG ▴ 350

Simply remove the cell type from the model. design <- model.matrix(~targets$Status)

Answer: ANOVA like approach of edgeR by Yunshun Chen ▴ 880

You could try the followings: > design <- model.matrix(~ 0 + group) > contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…

Answer: Identical samples after deseq2 batch effect removal by maripane • 0

Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…

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Answer: ANOVA like approach of edgeR

A: ANOVA-like test with edgeR

Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data

A: TopGO: How to retrieve the gene list related to a GO ID ?

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