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8
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10
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25k
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Design formula and Design matrix in DESeq
rnaseq
deseq2
formula
Limma
8.9 years ago
AurelieMLB
▴ 50
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
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
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
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
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
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
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
0
votes
1
reply
726
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
11 results • Page
1 of 1
Recent ...
Replies
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…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Comment: DEG Filtering
by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
Votes
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
Circumvent creating .ff files in the working directory when using genotype.Illumina() function
Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
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Pierre Lindenbaum
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★ 2.0k
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★ 3.1k
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