Bioconductor MultipleComparison

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209

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limmaGUI lim MultipleComparison multip

updated 9 weeks ago by Gordon Smyth 50k • written 9 weeks ago by roger.moreno.justicia • 0

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675

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Linnorm DEG MultipleComparison

updated 6 months ago by shunyip • 0 • written 2.7 years ago by awakumaya • 0

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711

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Proteomics proDA MultipleComparison

7 months ago t.b.n.nguyen-9 • 0

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642

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MultipleComparison DESeq2 Genetics contrasts RNASeq

updated 9 months ago by James W. MacDonald 65k • written 9 months ago by a26fd14e • 0

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656

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DESeq2 MultipleComparison r

updated 16 months ago by Michael Love 41k • written 16 months ago by ncorak • 0

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544

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MultipleComparison DESeq2

updated 23 months ago by Michael Love 41k • written 23 months ago by Joshua • 0

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2.2k

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MultipleComparison edgeR DESeq2

written 2.1 years ago by yuet • 0

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661

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factor DESeq2 MultipleComparison

updated 2.4 years ago by swbarnes2 ★ 1.3k • written 2.4 years ago by diegocastano182 • 0

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954

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GeneExpression R limma MultipleComparison

updated 3.4 years ago by James W. MacDonald 65k • written 3.4 years ago by Gwénolé • 0

9 results • Page 1 of 1

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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k

> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …

Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10

With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.

Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k

Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…

Comment: get BM error by James W. MacDonald 65k

I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…

Votes

Answer: How to retrieve gene ontology GO class from gene list?

C: when to apply quantile normalization with voom in limma/voom framework with RNA-

A: How to know if I should use voomWithQualityWeights() or not?

A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom

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