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Design formula and Design matrix in DESeq
rnaseq
deseq2
formula
Limma
8.9 years ago
AurelieMLB
▴ 50
0
votes
8
replies
1.9k
views
Two controls in RNAseq formula for DESeq2
deseq2
formula
controls
design
updated 4.6 years ago by
Michael Love
41k • written 4.6 years ago by
taveluz
• 0
3
votes
7
replies
1.7k
views
DESeq2 design formula: how to account for twin data (MZ and DZ)?
DESeq2
twins
design
formula
RNA-seq
6.4 years ago
Simone
• 0
0
votes
5
replies
1.5k
views
Limma: how to account for twin data (both MZ and DZ twins)?
limma
design
RNA-seq
formula
twins
updated 6.4 years ago by
Aaron Lun
★ 28k • written 6.4 years ago by
Simone
• 0
3
votes
8
replies
1.9k
views
Differential drug dosage effect between two genotypes in limma
limma
dose-response
linear model
model
formula
updated 6.3 years ago by
James W. MacDonald
65k • written 6.3 years ago by
biominer
▴ 10
0
votes
5
replies
1.2k
views
DESeq2 design formula - correlation with ordered variable
DESeq2
design
formula
matrix
updated 5.8 years ago by
Michael Love
41k • written 5.8 years ago by
t.kuilman
▴ 170
0
votes
6
replies
1.3k
views
variancePartition - testing for individuals
variance
formula
expression
updated 5.2 years ago by
mikhael.manurung
▴ 270 • written 5.2 years ago by
rina
▴ 30
0
votes
10
replies
2.3k
views
DEseq2 design formula correcting for batch
deseq2
design
formula
batch effect
updated 4.1 years ago by
swbarnes2
★ 1.3k • written 4.1 years ago by
l.rijnberk
• 0
0
votes
1
reply
727
views
DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2
design
formula
updated 3.4 years ago by
Michael Love
41k • written 3.4 years ago by
Bine
▴ 40
0
votes
1
reply
909
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 19 months ago by
Michael Love
41k • written 19 months ago by
estafana.t98
• 0
5
votes
6
replies
2.2k
views
Translating model formula from DESeq to DEXSeq
dexseq
linear model
formula
updated 8.4 years ago by
Alejandro Reyes
★ 1.9k • written 8.4 years ago by
Cornwell, Adam
▴ 110
11 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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