Bioconductor Nested

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DESeq2 multifactorial nested

updated 2.1 years ago by Basti ▴ 780 • written 2.1 years ago by jd • 0

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nested DESeq2

updated 3.2 years ago by Michael Love 43k • written 3.3 years ago by yampolsk • 0

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1.4k

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deseq2 Phyloseq Nested

updated 5.1 years ago by Michael Love 43k • written 5.1 years ago by mpuli011 • 0

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deseq2 Paired Nested

updated 5.3 years ago by Michael Love 43k • written 5.3 years ago by julia.chariker ▴ 10

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1.3k

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deseq2 nested de

updated 5.4 years ago by Michael Love 43k • written 5.4 years ago by gaio.transposon • 0

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1.6k

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edgeR nested glm glmQLFit

updated 6.0 years ago by Aaron Lun ★ 28k • written 6.0 years ago by jcalis ▴ 10

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edger nested design matrix differential expression

updated 10.2 years ago by Aaron Lun ★ 28k • written 10.2 years ago by Mauve • 0

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2.2k

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edger nested estimatedispersions

10.2 years ago Mauve • 0

8 results • Page 1 of 1

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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=…

Comment: edgeR::cpm() results in negative values from raw counts of 0 by Leonardo Collado Torres ★ 1.1k

Thanks for posting this Kinnary. See also https://github.com/LieberInstitute/spatialLIBD/issues/106 for more details on the background.

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

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

Comment: Differential expression analysis using two TCGA datasets

C: Annotating HTA 2.0 genes

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