Bioconductor PlotPCA

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1.0k

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Rstudio plotPCA DESeq2

17 months ago • updated 16 months ago yee • 0

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1.3k

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plotMA ggplot2 plotPCA DESeq2

updated 18 months ago by Michael Love 43k • written 18 months ago by sara.jacobson • 0

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5.7k

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plotPCA PCA

updated 2.0 years ago by hediatnani • 0 • written 2.1 years ago by Yijing • 0

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3.4k

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DESeq2 plotPCA

updated 10 months ago by Daniele • 0 • written 3.2 years ago by synat.keam • 0

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9.8k

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plotpca DESeq2

3.3 years ago bjen731 ▴ 10

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1.9k

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plotPCA DESeq2 RUVSeq removebatcheffect()

4.0 years ago elizabethe819 • 0

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1.2k

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DESeq2 RNASeq plotpca

updated 4.2 years ago by Michael Love 43k • written 4.2 years ago by s1760083 • 0

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1.4k

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deseq2 biplot plotpca

updated 5.2 years ago by Michael Love 43k • written 5.2 years ago by ecg1g15 ▴ 30

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836

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deseq2 PlotPCA draw.triple.venn

updated 6.6 years ago by Michael Love 43k • written 6.6 years ago by N. Perera • 0

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860

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deseq2 plotpca

updated 6.6 years ago by Michael Love 43k • written 6.6 years ago by snp31 • 0

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8.2k

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deseq2 plotpca PCa

updated 7.5 years ago by Michael Love 43k • written 7.5 years ago by lirongrossmann ▴ 80

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3.9k

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deseq2 rlog variancestabilizingtransformation plotpca pca

7.6 years ago lirongrossmann ▴ 80

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3.6k

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DESeq2 plotPCA rlog transformation vsd

7.7 years ago Jane Merlevede ▴ 90

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48k

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plotPCA deseq2 labels

updated 8.3 years ago by Federico Marini ▴ 180 • written 8.3 years ago by al-ash ▴ 50

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pca plotpca

8.5 years ago marianarochadesouza • 0

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1.8k

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deseq2 plotPCA PCA rna-seq

8.9 years ago newsomew13 • 0

16 results • Page 1 of 1

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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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