Biostar CBioPortalData

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cBioPortalData

updated 21 months ago by Marcel Ramos 620 • written 21 months ago by andreas.wernitznig • 0

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cBioPortalData

5 months ago ryan.hagenson • 0

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RaggedExperiment cBioPortalData

updated 5 months ago by Marcel Ramos 620 • written 5 months ago by ryan.hagenson • 0

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MultiAssayExperiment cBioPortalData

updated 21 months ago by Kevin Blighe 3.7k • written 21 months ago by Javier • 0

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Answer: collapseReplicates error after tximeta by Michael Love 39k

The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…

Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it by ATpoint ★ 2.1k

That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…

Answer: Which genes are outliers in DESeq2? by ATpoint ★ 2.1k

You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…

Answer: Which genes are outliers in DESeq2? by Michael Love 39k

Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…

Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it by Michael Love 39k

Specifying `controlGenes` means it estimates the size factors over those rows. But size factors when used later as offsets in GLM or when u…

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Significant reporter activity with mpralm function

Answer: I cannot install annotables package in Rstudio (macOS)

Answer: log2 of normalized counts for further analyzes

Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it

Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used

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