Bioconductor Foldchange

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2.3k

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EdgeR RNAseq Foldchange

updated 2.8 years ago by swbarnes2 ★ 1.3k • written 2.8 years ago by najib • 0

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2.3k

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foldchange topGO DifferentialExpression enrichment

updated 3.4 years ago by Gordon Smyth 50k • written 3.5 years ago by lessismore ▴ 20

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4.7k

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DifferentialExpression DEA FC FoldChange edgeR

2.6 years ago zhxiaokang ▴ 20

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1.4k

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limma microarray foldchange DEG GEO

updated 4.2 years ago by Gordon Smyth 50k • written 4.2 years ago by Pietro ▴ 40

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1.4k

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limma RNAseq foldchange

5.2 years ago • updated 5.1 years ago susana.amaral.teixeira ▴ 20

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790

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FoldChange DiffBind lfcShrink Cut&TagData

10 months ago bhandary.8590 ▴ 20

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1.5k

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DESeq2 TPM Foldchange

updated 2.1 years ago by Michael Love 41k • written 2.1 years ago by dadca596 • 0

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430

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StatisticalMethod FoldChange edgeR RNASeq

4 months ago Sabiha ▴ 20

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1.1k

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sign FoldChange DESeq2 reference

updated 2.3 years ago by Michael Love 41k • written 2.3 years ago by yampolsk • 0

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2.2k

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FoldChange DiffBind lfcShrink

updated 9 months ago by Rory Stark ★ 5.1k • written 9 months ago by bhandary.8590 ▴ 20

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884

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edgeR RNA-Seq log2 foldchange q_value

updated 2.3 years ago by Gordon Smyth 50k • written 2.3 years ago by johndavidgriner74 • 0

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1.3k

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DEXSeq DTU salmon rnaseqDTU foldchange

updated 5.0 years ago by Michael Love 41k • written 5.3 years ago by fiona.dick91 ▴ 60

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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

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

Answer: Log-cpm values from limma

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