Bioconductor PlotMA

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610

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plotMA ggplot2 plotPCA DESeq2

updated 6 months ago by Michael Love 41k • written 6 months ago by sara.jacobson • 0

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615

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matrixsubset DESeq2 plotMA

updated 3.0 years ago by Michael Love 41k • written 3.0 years ago by l.troxler ▴ 10

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877

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deseq2 plotMA rnaseq community analysis asymmetry

updated 4.2 years ago by Michael Love 41k • written 4.2 years ago by chaco001 • 0

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956

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agilent single channel plotMA background correction

updated 5.9 years ago by Gordon Smyth 50k • written 5.9 years ago by CantExitVIM ▴ 10

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1.1k

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deseq2 plotMA rnaseq logfoldchange

updated 6.2 years ago by Michael Love 41k • written 6.2 years ago by ap_vc21 • 0

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2.6k

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deseq2 plotma

6.6 years ago Yvan Wenger ▴ 50

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4.9k

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rstudio r plotMA

6.9 years ago g.k • 0

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4.8k

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deseq2 rnaseq plotMA deseq rna-seq

updated 8.1 years ago by Michael Love 41k • written 8.1 years ago by sjs0282 • 0

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3.7k

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limma plotMA

updated 8.7 years ago by Gordon Smyth 50k • written 8.7 years ago by Lisa Cohen ▴ 50

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2.4k

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normalization deseq2 plotMA meanSDplot

8.7 years ago aravenscraft • 0

10 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

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

Awards • All

Supporter to Jonathan ▴ 10