Bioconductor Epic microarray

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champ epic microarray normalization minfi

6.9 years ago Laura • 0

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minfi epic microarray bioconductor

updated 2.8 years ago by Lucy • 0 • written 7.1 years ago by c.sae-lee2 • 0

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bioconductor methylation epic microarray champ

7.3 years ago csappleby-mallinder1 • 0

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methylation epic microarray minfi methylationepic

8.1 years ago nhejazi • 0

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shinymethyl minfi epic microarray methylationepic qualitycontrol

8.2 years ago chelsey.ju • 0

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rnbeads methylation illumina epic microarray

8.7 years ago rasii • 0

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minfi dmpfinder dmp illuminahumanmethylationepicanno.ilmn10b.hg19 epic microarray

updated 8.8 years ago by James W. MacDonald 68k • written 8.8 years ago by Biologist ▴ 120

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1.9k

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minfi methylation EPIC microarray illumina

updated 9.0 years ago by Kasper Daniel Hansen ★ 6.5k • written 9.0 years ago by rasii • 0

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Comment: edgeR::cpm() results in negative values from raw counts of 0 by Paul Harrison ▴ 100

One purely practical advantage to keeping zeros zero in particular is that sparse matrices stay sparse (using the `log1p` function). I thin…

Answer: edgeR::cpm() results in negative values from raw counts of 0 by Gordon Smyth 52k

**logCPM values decrease as the library size increases** `edgeR::cpm` computes logCPM values according to the formula `log2( (y + y0) / (L…

Comment: edgeR::cpm() results in negative values from raw counts of 0 by Gordon Smyth 52k

Thanks answering this question. Let me say though that I've never understood why people would find negative log values to be annoying or un…

Answer: edgeR::cpm() results in negative values from raw counts of 0 by ATpoint ★ 4.8k

The function, when `log = TRUE` adds a small prior count to the counts before taking the log, avoiding taking the log of 0. If that prior i…

Answer: edgeR::cpm() results in negative values from raw counts of 0 by James W. MacDonald 68k

It's calculated exactly how you might expect (it's called counts/million counts for a reason). ``` > y <- matrix(rnbinom(20,size=1,mu=…

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edgeR::cpm() results in negative values from raw counts of 0

Answer: edgeR::cpm() results in negative values from raw counts of 0

Comment: edgeR::cpm() results in negative values from raw counts of 0

Answer: edgeR::cpm() results in negative values from raw counts of 0

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