Biostar Onechannel

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3.0k

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Microarray OneChannel TwoChannel DataImport bridge GEOquery Microarray OneChannel bridge

updated 15.3 years ago by Sean Davis 21k • written 15.3 years ago by Wittner, Ben ▴ 290

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1.2k

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Microarray OneChannel Annotation Normalization probe Biobase annotate genefilter affy vsn

updated 14.2 years ago by Pan Du ★ 1.2k • written 14.2 years ago by Steve Taylor ▴ 280

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1.3k

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limma microarray onechannel red custom

updated 7.4 years ago by Gordon Smyth 47k • written 7.4 years ago by dario.veneziano • 0

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875

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Microarray OneChannel TwoChannel DifferentialExpression Preprocessing QualityControl affy

15.7 years ago Amin Moghaddasi ▴ 130

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2.5k

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wgcna twochannel onechannel

updated 8.2 years ago by Peter Langfelder ★ 2.7k • written 8.2 years ago by jeiroje ▴ 20

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541

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OneChannel OneChannel

11.7 years ago Guido Leoni ▴ 200

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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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