Bioconductor Gene ontology level

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clusterprofiler groupGO gene ontology level

updated 7.0 years ago by Guangchuang Yu ★ 1.2k • written 7.0 years ago by saadmurtazakhan ▴ 10

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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.

Answer: Gene Ontology (GO) Analysis by James W. MacDonald 68k

The main difference is that `enrichGO` fits a conventional hypergeometric test whereas `hyperGTest` allows you to do a conditional test as …

Comment: blockwiseModule crashes in the end and doesn't generate modules by drivingdirectionsonline • 0

Solution: The error is likely due to a conflicting cor() function from another package (like psych). Restart R, run blockwiseModules() befo…

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C: Annotating HTA 2.0 genes

A: Annotating HTA 2.0 genes

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