Bioconductor Blocking

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687

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voom blocking limma

updated 6 months ago by Gordon Smyth 50k • written 6 months ago by Gerhard Thallinger ▴ 180

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692

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edgeR blocking

updated 3.0 years ago by Yunshun Chen ▴ 840 • written 3.0 years ago by Molly • 0

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922

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diffbind blocking model

updated 3.5 years ago by Rory Stark ★ 5.1k • written 4.5 years ago by melnuesch ▴ 10

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1.4k

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edger limma paired blocking ruvseq

updated 3.9 years ago by Gordon Smyth 50k • written 3.9 years ago by ScA • 0

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1.9k

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limma repeated measurements blocking random effects

updated 4.2 years ago by Gordon Smyth 50k • written 4.2 years ago by Jane ▴ 10

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3.6k

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limma edger blocking paired samples

updated 5.4 years ago by Gordon Smyth 50k • written 5.4 years ago by anou ▴ 10

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806

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diffbind differential binding analysis blocking

updated 6.3 years ago by Rory Stark ★ 5.1k • written 6.3 years ago by zhangly811 • 0

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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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