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design
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0
votes
0
replies
40
views
Limma: twin study with mono & dizygotic, discordant and concordant pairs
twins
limma
formula
design
11 days ago
Geoff
• 0
0
votes
1
reply
485
views
edgeR - design a complex matrix
design
model.matrix
edgeR
complexdesign
updated 7 months ago by
Gordon Smyth
52k • written 7 months ago by
Karla
• 0
3
votes
3
replies
882
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 10 months ago by
Gordon Smyth
52k • written 10 months ago by
Guillermo
• 0
0
votes
6
replies
866
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 10 months ago by
swbarnes2
★ 1.4k • written 10 months ago by
arfranco
▴ 130
2
votes
3
replies
778
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 12 months ago by
Gordon Smyth
52k • written 12 months ago by
JKim
• 0
2
votes
2
replies
622
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
12 months ago
Sabiha
▴ 20
2
votes
2
replies
591
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design
limma
13 months ago
SamGG
▴ 360
3
votes
6
replies
1.3k
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 22 months ago by
Gordon Smyth
52k • written 22 months ago by
mohammedtoufiq91
▴ 10
3
votes
9
replies
2.8k
views
Question about filter by expression (filterByExpr) in edgeR
CPM
filterByExpr
edgeR
design
model.matrix
24 months ago
mohammedtoufiq91
▴ 10
6
votes
11
replies
2.0k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR
DifferentialExpression
limma
design
RNASeq
2.1 years ago
mohammedtoufiq91
▴ 10
2
votes
2
replies
1.2k
views
Updating DESeq2 object's design with sva output
DESeq2
design
sva
2.1 years ago
Hatchet
• 0
3
votes
6
replies
1.6k
views
Question about making Contrasts for comparisons and assignment of values
edgeR
contrasts
limma
design
model.matrix
2.3 years ago
mohammedtoufiq91
▴ 10
1
vote
2
replies
1.1k
views
Extracting specific comparisons after fitting model in EdgeR
edgeR
limma
design
RNASeq
model.matrix
2.3 years ago
mohammedtoufiq91
▴ 10
1
vote
2
replies
1.0k
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma
R
design
model.matrix
2.3 years ago
mohammedtoufiq91
▴ 10
0
votes
13
replies
3.0k
views
DESeq2 design multi factor
DESeq2
design
0substract
nofullrank
updated 2.4 years ago by
Michael Love
43k • written 2.4 years ago by
Laia
▴ 10
0
votes
5
replies
1.4k
views
Inquiry about suitable package for proteomics study design
Proteomics
design
updated 2.4 years ago by
evocanres
• 0 • written 2.4 years ago by
proteome_AO
• 0
2
votes
5
replies
4.2k
views
DESeq2 with two continuous variable in a design
DESeq2
RNASeq
R
design
updated 2.4 years ago by
Michael Love
43k • written 3.7 years ago by
sofia
• 0
0
votes
1
reply
807
views
Design Matrix Singularity Error
DES
DESIGN
updated 2.5 years ago by
Michael Love
43k • written 2.5 years ago by
mike
• 0
0
votes
2
replies
918
views
Design set up, interaction or group? Two Salinities treatments, Five Populations, Three Replicates
Design
DESeq2
updated 2.8 years ago by
Michael Love
43k • written 2.8 years ago by
lgspeight
• 0
2
votes
2
replies
2.3k
views
Handling NA values in limma's voom design matrix
limma
voom
design
NAs
updated 2.9 years ago by
Gordon Smyth
52k • written 2.9 years ago by
dr
▴ 10
0
votes
4
replies
1.3k
views
DESeq2 pseudotime series design?
DESeq2
design
3.1 years ago
jordi.planells
• 0
0
votes
2
replies
1.1k
views
DeSeq2 - design formula for enrichment on combinated conditions AB, not A, not B
conditions
design
DESeq2
Synergy
updated 3.3 years ago by
Michael Love
43k • written 3.3 years ago by
johannesdolberg
• 0
0
votes
1
reply
1.0k
views
Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast
design
DESeq2
continuous
updated 3.3 years ago by
Michael Love
43k • written 3.3 years ago by
tiansy
• 0
1
vote
1
reply
1.0k
views
Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment
RNASeq
design
DESeq2
updated 3.3 years ago by
Michael Love
43k • written 3.3 years ago by
Kesava
• 0
1
vote
2
replies
1.4k
views
Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq
Design
Matrix
3.4 years ago
Barista
• 0
0
votes
2
replies
1.3k
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions
design
Multifactorial
DESeq2
updated 3.4 years ago by
swbarnes2
★ 1.4k • written 3.4 years ago by
Marie
• 0
0
votes
1
reply
829
views
Account for parent cell line when comparing isogenic mutants
interactions
design
DESeq2
updated 3.4 years ago by
Michael Love
43k • written 3.4 years ago by
oliver.ziff
• 0
0
votes
2
replies
1.3k
views
Design formula in DESeq2
model
BatchEffect
hidden
Design
DESeq2
3.4 years ago
m.glymenaki
• 0
2
votes
3
replies
1.8k
views
Contrast treated samples against both scramble and untreated controls
design
contrast
DESeq2
updated 3.4 years ago by
Michael Love
43k • written 3.4 years ago by
oliver.ziff
• 0
0
votes
1
reply
2.3k
views
DESeq2 time course and dosage response
LRT
Design
DESeq2
doseResponse
TimeSeriesExperiment
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
Mari
• 0
0
votes
1
reply
1.2k
views
Subject paired DESeq2 design
DESeq2
paired
design
updated 3.6 years ago by
Michael Love
43k • written 3.6 years ago by
dr
▴ 10
0
votes
1
reply
911
views
[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2
nesting
design
updated 3.7 years ago by
Michael Love
43k • written 3.7 years ago by
christophe.vanhaver
• 0
2
votes
3
replies
1.6k
views
Differential expression error in edgeR - maybe from design matrix?
design
edgeR
matrix
RNA-seq
MDplot
updated 3.8 years ago by
Gordon Smyth
52k • written 3.8 years ago by
Alex
• 0
2
votes
3
replies
10k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions
DESeq2
Design
updated 4.2 years ago by
Kevin Blighe
★ 4.0k • written 4.2 years ago by
vanbelj
▴ 30
0
votes
1
reply
937
views
DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2
design
formula
updated 4.4 years ago by
Michael Love
43k • written 4.4 years ago by
Bine
▴ 50
2
votes
3
replies
1.1k
views
EdgeR design matrix for mutlifactor RNA seq
edger
design
multifactor
updated 4.4 years ago by
James W. MacDonald
68k • written 4.4 years ago by
jackiesalzbank
• 0
0
votes
5
replies
2.3k
views
DESeq2 issue with hierarchical clustering
deseq2
design
updated 4.5 years ago by
Kevin Blighe
★ 4.0k • written 4.5 years ago by
mhnidhi2-c
• 0
2
votes
5
replies
1.5k
views
Picking the right design formula
deseq2
design
experiment
4.5 years ago
donnenfieldjonah
• 0
4
votes
5
replies
3.7k
views
How to incorporate batch effect that is only present in one level into the design?
linear model
batch effect
DESeq2
design
updated 4.6 years ago by
James W. MacDonald
68k • written 4.6 years ago by
tim.meese
• 0
2
votes
8
replies
5.4k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma
deseq2
batch
design
batch effect
4.6 years ago
Pietro
▴ 40
4
votes
7
replies
1.5k
views
Genes upregulated in one condition vs each of the other conditions
edger
design
updated 4.7 years ago by
Gordon Smyth
52k • written 4.7 years ago by
dario.beraldi
• 0
0
votes
1
reply
1.1k
views
Coefficients not estimable voom Lima with multiple numeric covariate
r
limma
design
rnaseq
voom
updated 4.8 years ago by
Gordon Smyth
52k • written 4.8 years ago by
Will
• 0
2
votes
7
replies
2.6k
views
Limma analysis with multiple variables
limma
model.matrix
de
design
rnaseq
updated 4.8 years ago by
Gordon Smyth
52k • written 4.8 years ago by
Will
• 0
6
votes
6
replies
1.6k
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq
design
linear model
glm
updated 5.1 years ago by
Steve Lianoglou
★ 13k • written 5.1 years ago by
tmms
• 0
0
votes
10
replies
3.4k
views
DEseq2 design formula correcting for batch
deseq2
design
formula
batch effect
updated 5.1 years ago by
swbarnes2
★ 1.4k • written 5.1 years ago by
l.rijnberk
• 0
1
vote
4
replies
1.1k
views
Help with Deseq2 design
deseq2
design
multifactor
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
sxp585
• 0
1
vote
1
reply
28k
views
lfcShrink doesn't work with contrasts
lfcShrink
contrast
design
deseq2
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
1.4k
views
Design of time-course experiment in DESeq2
deseq2
design
design formula
time course
lrt
updated 5.2 years ago by
Michael Love
43k • written 5.2 years ago by
ac_bioinformatics
• 0
2
votes
1
reply
1.7k
views
combining columns for experimental design in DESeq2
deseq2
design
metadata
updated 5.2 years ago by
sebastian.lobentanzer
▴ 60 • written 5.2 years ago by
Assa Yeroslaviz
★ 1.5k
1
vote
8
replies
9.7k
views
DESeq2: Continuous and discreate variables in the design
deseq2
R
rna-seq
design
updated 4.2 years ago by
Michael Love
43k • written 5.3 years ago by
raquelgarza95
• 0
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Answer: Improving performance of edgeR and limma while adjusting for multiple confounder
by
Gordon Smyth
52k
We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…
Answer: Merging EPICV1 and V2 betas
by
James W. MacDonald
68k
It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…
Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species
by
Benjamin
▴ 20
I have received a response from Ensembl regarding the items I have listed above. I wanted to post it here and will continue to post update…
Answer: Error in cnetplot
by
Guido Hooiveld
★ 4.1k
Unfortunately you did not show how you generated your input data (the object `enrichment`), nor did you show the output from `sessionInfo()…
Answer: getBM from biomaRt inconsistencies found with .gtf files across multiple species
by
Mike Smith
★ 6.6k
I think this is because Ensembl can assign different Gene IDs to "the same gene" if it is found both on a standard chromosome and a scaffol…
Votes
Answer: Explannation for ROAST results
Comment: Limma comparing gene expression between base line and one treatment
Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?
clusterProfiler-GO enrichment Error
A: Machine learning in R book
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