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8
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Design formula and Design matrix in DESeq
rnaseq
deseq2
formula
Limma
9.0 years ago
AurelieMLB
▴ 50
5
votes
6
replies
2.3k
views
Translating model formula from DESeq to DEXSeq
dexseq
linear model
formula
updated 8.5 years ago by
Alejandro Reyes
★ 1.9k • written 8.5 years ago by
Cornwell, Adam
▴ 110
3
votes
8
replies
2.0k
views
Differential drug dosage effect between two genotypes in limma
limma
dose-response
linear model
model
formula
updated 6.4 years ago by
James W. MacDonald
65k • written 6.4 years ago by
biominer
▴ 10
3
votes
7
replies
1.8k
views
DESeq2 design formula: how to account for twin data (MZ and DZ)?
DESeq2
twins
design
formula
RNA-seq
6.5 years ago
Simone
• 0
0
votes
8
replies
2.0k
views
Two controls in RNAseq formula for DESeq2
deseq2
formula
controls
design
updated 4.7 years ago by
Michael Love
42k • written 4.7 years ago by
taveluz
• 0
0
votes
10
replies
2.4k
views
DEseq2 design formula correcting for batch
deseq2
design
formula
batch effect
updated 4.3 years ago by
swbarnes2
★ 1.3k • written 4.3 years ago by
l.rijnberk
• 0
0
votes
1
reply
755
views
DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2
design
formula
updated 3.5 years ago by
Michael Love
42k • written 3.5 years ago by
Bine
▴ 40
0
votes
1
reply
975
views
Batch effects in DESeq2: determination and model building
BatchEffect
batch
RNASeqR
formula
DESeq2
updated 20 months ago by
Michael Love
42k • written 20 months ago by
estafana.t98
• 0
0
votes
5
replies
1.6k
views
Limma: how to account for twin data (both MZ and DZ twins)?
limma
design
RNA-seq
formula
twins
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
Simone
• 0
0
votes
5
replies
1.3k
views
DESeq2 design formula - correlation with ordered variable
DESeq2
design
formula
matrix
updated 5.9 years ago by
Michael Love
42k • written 5.9 years ago by
t.kuilman
▴ 170
0
votes
6
replies
1.3k
views
variancePartition - testing for individuals
variance
formula
expression
updated 5.3 years ago by
mikhael.manurung
▴ 270 • written 5.3 years ago by
rina
▴ 30
11 results • Page
1 of 1
Recent ...
Replies
Comment: Cannot connect to ExperimentHub server
by
Jiayu
• 0
Many thanks and it also resolved the same issue for me!
Comment: Help with running egsea()
by
Chris
• 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
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42k
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