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R studio input style for generating heatmap (RNAseq)
heatmap r studio log2foldchange
updated 5.2 years ago by ★ 13k • written 5.2 years ago by • 0
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> DBdata <-dba(sampleSheet = samples) Error: object of type 'closure' is not subsettable
DiffBind R R Studio
updated 5.8 years ago by 68k • written 5.8 years ago by ▴ 10
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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
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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