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factor
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5
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DESeq2 with multiple variable give me different results
Factor
Levels
Dispersionestimates
DESeq2
2.4 years ago
rafaelsolersanblas
▴ 50
3
votes
11
replies
3.4k
views
DESeq function taking too long
deseq2
deseq
factor
rnaseq
updated 6.7 years ago by
Peter Langfelder
★ 2.9k • written 6.7 years ago by
sup230
▴ 30
2
votes
3
replies
1.6k
views
GenomicRanges_RaggedExperiment Error in as background, class mcol no method or default for coercing logical to factor
genomicranges
RaggedExperiment
coercion
logical
factor
updated 6.4 years ago by
Marcel Ramos
690 • written 6.4 years ago by
Taran
• 0
2
votes
2
replies
1.4k
views
How to extract factor levels of coldata from deseq object?
deseq2
levels
factor
colData
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
ariel
▴ 20
0
votes
2
replies
1.7k
views
GenomicRanges: `seqnames<-` can not work as expected
genomicranges
seqnames
factor
7.4 years ago
wcstcyx
▴ 30
0
votes
1
reply
628
views
DESeq2: Difference between two groups of conditions
factor
DESeq2
MultipleComparison
updated 2.4 years ago by
swbarnes2
★ 1.3k • written 2.4 years ago by
diegocastano182
• 0
0
votes
0
replies
800
views
Package in R to determine which factor values are overrepresented within a particular factor of interest
R
overrrepresentation
factor
variable
factor enrichment
7.4 years ago
IOM
▴ 20
7 results • Page
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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