Bioconductor Methods

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BSgenome methods GenomicRanges

3.7 years ago Aditya ▴ 160

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527

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S4Vectors methods

3.7 years ago Aditya ▴ 160

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s4 methods SummarizedExperiment

updated 4.3 years ago by Aaron Lun ★ 28k • written 4.3 years ago by brendan.innes ▴ 10

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757

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devtools S4 methods cache

4.5 years ago Michael Steinbaugh ▴ 90

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611

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deconvolution methods

5.3 years ago casey.rimland ▴ 150

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Comment: Visualization of negative log CPM values by Gordon Smyth 47k

Sorry, but some of the things you say are not correct. > compound B has 2 statistically significant genes that are up-regulated No, there…

Comment: Visualization of negative log CPM values by ATpoint ★ 2.8k

Applies to both.

Comment: Visualization of negative log CPM values by Sabiha ▴ 10

@atpoint OK, are you referring to the `log2(cpm+1)` or `log2(tpm+1)`

Comment: Visualization of negative log CPM values by Sabiha ▴ 10

@gordonsmyth noted. Related to the graphs above, the table below is the output from `limma`, and compound B has 2 statistically significant…

Comment: Visualization of negative log CPM values by Gordon Smyth 47k

> negative scale might perhaps indicate gene is too low to be really expressed. Yes, negative logCPMs do mean that the gene is expressed a…

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Comment: Visualization of negative log CPM values

Any efficient workaround to identify highly variable genes in Affymetrix microarray expression data?

Filtering low intensity probes in microarray data

Comment: Visualization of negative log CPM values

Adjusting for baseline when having longitudinal data, mixed model and no treatment

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