Bioconductor BioNERO

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plot_expression_profile BioNERO

18 months ago Christopher ▴ 20

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BioNERO

20 months ago matevz.likar • 0

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#BioNERO BioNERO Cystoscope

updated 2.1 years ago by Fabricio Almeida-Silva ▴ 40 • written 2.1 years ago by Hasani • 0

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GRN BioNERO

updated 2.1 years ago by Fabricio Almeida-Silva ▴ 40 • written 2.2 years ago by majeedaasim • 0

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BioNERO Pviz

2.3 years ago • updated 2.2 years ago zxd95 • 0

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BioNERO

updated 2.5 years ago by Fabricio Almeida-Silva ▴ 40 • written 2.5 years ago by Biologist • 0

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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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