Bioconductor Champdata

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ChAMPdata ChAMP

updated 6 weeks ago by James W. MacDonald 65k • written 12 months ago by angel • 0

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139

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ChAMPdata IlluminaHumanMethylationEPICv2anno.20a1.hg38 ChAMP

updated 2 days ago by James W. MacDonald 65k • written 6 days ago by Mirella Aurora • 0

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ChAMPdata ChAMP

updated 2.3 years ago by Basti ▴ 780 • written 2.3 years ago by mariat • 0

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1.2k

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ChAMP limma Bioconductor ChAMPdata

2.7 years ago • updated 2.6 years ago Jinyue • 0

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1.2k

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loaddata ChAMPdata champload R ChAMP

updated 11 months ago by hfbarrerat • 0 • written 3.2 years ago by Bethan • 0

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866

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Illumina methylationArrayAnalysis ChAMPdata ChAMP

3.2 years ago sissialva21 • 0

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1.2k

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ChAMP ChAMPdata

updated 3.0 years ago by shepherl 3.8k • written 3.0 years ago by Federica ▴ 10

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780

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ChAMP shiny ChAMPdata

updated 2.1 years ago by anna.stanislawska • 0 • written 2.1 years ago by Mari • 0

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192

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ChAMPdata ChAMP

9 weeks ago Meghana • 0

9 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

Teacher to Gordon Smyth 50k