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singscore
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'combined score' calculation with singscore vs gsva
singscore
GSVA
3 months ago • updated 11 weeks ago
rocanja
▴ 60
0
votes
1
reply
429
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Error in "generateNull" with only one set of gene list
singscore
generateNull
updated 2.1 years ago by
bhuva.d
• 0 • written 2.8 years ago by
tiphaine.martin
• 0
2
votes
4
replies
1.4k
views
Are singscore scores comparable between gene sets?
singscore
GSVA
GSEA
subtypes
geneset
updated 2.1 years ago by
bhuva.d
• 0 • written 3.9 years ago by
Pietro
▴ 40
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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…
Votes
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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Guido Hooiveld
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