Showing : coef • reset
2
votes
3
replies
2.7k
views
lfcshrink() with no coef in resultsNames()
lfcshrink coef DESeq2
updated 3.5 years ago by 43k • written 4.4 years ago by ★ 1.5k
0
votes
3
replies
2.3k
views
glmQLFTest, coef=2:4, decideTestDGE not working
edger DGE coef
updated 7.5 years ago by ★ 28k • written 7.5 years ago by • 0
17
votes
7
replies
15k
views
DESeq2 lfcShrink() usage of coef vs. usage of contrast
deseq2 lfc coef contrast
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 10
0
votes
8
replies
2.1k
views
ReportingTools include pvalue NA and comparissons
R reportingtools deseq2 pvalue coef
updated 8.9 years ago by 43k • written 8.9 years ago by ▴ 10
4 results • Page 1 of 1
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Comment: Bioconductor 3.20 Release Schedule by randyprice13102000 • 0
This offers much info https://bioconductor.org/checkResults/release/bioc-LATEST/
Comment: Filtering after DESeq by ATpoint ★ 4.8k
The problem is that your prefilter is not group-aware so the behaviour of seeing these sorts of outliers is expected. This is why I always …
Comment: GSEA preranked analysis downstream of DEseq2 by ATpoint ★ 4.8k
All due respect, this is what people do since pvalues exist, so this paper is not a reference, not is this a special score that merits a na…
Comment: Check removeBatchEffect effectiveness by ATpoint ★ 4.8k
> insert size, mean GC, etc... This is not a classical "batch" in the common sense, at least I've never seen this to be corrected for expl…
Answer: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Your call to removeBatchEffect() is not correct because that function does not have an argument called `batch3`, meaning that the batch fac…
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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