Bioconductor DEseq

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297

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DESeq2 deseq

8 weeks ago Meme • 0

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326

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deseq DESeq2

updated 4 months ago by ATpoint ★ 4.0k • written 4 months ago by Hugo • 0

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506

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deseq DESeq2

5 months ago georgii.vdovin • 0

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369

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Deseq DESeq2

updated 5 months ago by Michael Love 41k • written 5 months ago by georgii.vdovin • 0

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638

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Z-score RNASeqData Deseq DESeq2

updated 7 months ago by James W. MacDonald 65k • written 7 months ago by khaserdene99 • 0

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864

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DESeq DESeq2

updated 8 months ago by ATpoint ★ 4.0k • written 8 months ago by Abir.khazaal ▴ 10

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627

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DESeq2 apeglm DESeq ApeGLM Ashr

updated 9 months ago by Michael Love 41k • written 9 months ago by Ndimensional ▴ 20

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26k

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deseq deseq2

updated 8 months ago by Erika • 0 • written 9.2 years ago by c.lieftink@nki.nl ▴ 40

8 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…

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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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