Bioconductor Abarray

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GO genefilter limma GeneSpring ABarray preprocessCore arrayQualityMetrics GO genefilter

updated 12.8 years ago by Jenny Drnevich ★ 2.0k • written 12.8 years ago by Dana.Stanley@csiro.au ▴ 110

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Cancer ABarray Cancer ABarray

updated 14.8 years ago by SimonNoël ▴ 450 • written 14.8 years ago by Hervé Pagès 16k

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Microarray GO genefilter limma GeneSpring ABarray preprocessCore arrayQualityMetrics BRAIN

updated 12.8 years ago by Guillaume Meurice ▴ 210 • written 12.8 years ago by Dana.Stanley@csiro.au ▴ 110

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ABarray ABarray

updated 17.2 years ago by James W. MacDonald 65k • written 17.2 years ago by Alison Ziesel ▴ 60

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ABarray ABarray

updated 14.8 years ago by Thomas Hampton ▴ 750 • written 14.8 years ago by SimonNoël ▴ 450

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probe ABarray probe ABarray

12.2 years ago Iain Gallagher ▴ 930

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ABarray ABarray

updated 14.0 years ago by Heidi Dvinge ★ 2.0k • written 14.0 years ago by Brian Diggs ▴ 30

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883

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Abarray error ABI Human Genome Survey V2

6.2 years ago judemtaylor • 0

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ABarray ABarray

16.5 years ago Sabah Khalid ▴ 10

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ABarray ABarray

14.8 years ago Priyanka Jain ▴ 20

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ABarray ABarray

14.8 years ago Priyanka Jain ▴ 20

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GO TimeCourse genefilter timecourse ABarray preprocessCore GeneSelector GO TimeCourse

12.8 years ago Dennis.Burian@faa.gov ▴ 90

12 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