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DESIGN
•
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0
votes
6
replies
149
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 6 hours ago by
swbarnes2
★ 1.3k • written 1 day ago by
arfranco
▴ 130
2
votes
3
replies
292
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
JKim
• 0
2
votes
2
replies
259
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
7 weeks ago
Sabiha
▴ 20
2
votes
2
replies
286
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design
limma
12 weeks ago
SamGG
▴ 350
3
votes
6
replies
842
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
mohammedtoufiq91
▴ 10
3
votes
9
replies
1.8k
views
Question about filter by expression (filterByExpr) in edgeR
CPM
filterByExpr
edgeR
design
model.matrix
13 months ago
mohammedtoufiq91
▴ 10
6
votes
11
replies
1.4k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR
DifferentialExpression
limma
design
RNASeq
14 months ago
mohammedtoufiq91
▴ 10
2
votes
2
replies
837
views
Updating DESeq2 object's design with sva output
DESeq2
design
sva
14 months ago
Hatchet
• 0
3
votes
6
replies
993
views
Question about making Contrasts for comparisons and assignment of values
edgeR
contrasts
limma
design
model.matrix
16 months ago
mohammedtoufiq91
▴ 10
1
vote
2
replies
759
views
Extracting specific comparisons after fitting model in EdgeR
edgeR
limma
design
RNASeq
model.matrix
17 months ago
mohammedtoufiq91
▴ 10
1
vote
2
replies
787
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma
R
design
model.matrix
17 months ago
mohammedtoufiq91
▴ 10
0
votes
5
replies
1000
views
Inquiry about suitable package for proteomics study design
Proteomics
design
updated 18 months ago by
evocanres
• 0 • written 18 months ago by
proteome_AO
• 0
0
votes
13
replies
2.1k
views
DESeq2 design multi factor
DESeq2
design
0substract
nofullrank
updated 17 months ago by
Michael Love
41k • written 18 months ago by
Laia
▴ 10
0
votes
1
reply
567
views
Design Matrix Singularity Error
DES
DESIGN
updated 19 months ago by
Michael Love
41k • written 19 months ago by
mike
• 0
0
votes
2
replies
684
views
Design set up, interaction or group? Two Salinities treatments, Five Populations, Three Replicates
Design
DESeq2
updated 23 months ago by
Michael Love
41k • written 23 months ago by
lgspeight
• 0
2
votes
2
replies
1.5k
views
Handling NA values in limma's voom design matrix
limma
voom
design
NAs
updated 24 months ago by
Gordon Smyth
50k • written 24 months ago by
dr
▴ 10
0
votes
4
replies
985
views
DESeq2 pseudotime series design?
DESeq2
design
2.2 years ago
jordi.planells
• 0
0
votes
2
replies
861
views
DeSeq2 - design formula for enrichment on combinated conditions AB, not A, not B
conditions
design
DESeq2
Synergy
updated 2.4 years ago by
Michael Love
41k • written 2.4 years ago by
johannesdolberg
• 0
0
votes
1
reply
747
views
Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast
design
DESeq2
continuous
updated 2.4 years ago by
Michael Love
41k • written 2.4 years ago by
tiansy
• 0
1
vote
1
reply
798
views
Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment
RNASeq
design
DESeq2
updated 2.4 years ago by
Michael Love
41k • written 2.4 years ago by
Kesava
• 0
1
vote
2
replies
975
views
Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq
Design
Matrix
2.5 years ago
Barista
• 0
0
votes
2
replies
1.0k
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions
design
Multifactorial
DESeq2
updated 2.5 years ago by
swbarnes2
★ 1.3k • written 2.5 years ago by
Marie
• 0
0
votes
1
reply
615
views
Account for parent cell line when comparing isogenic mutants
interactions
design
DESeq2
updated 2.5 years ago by
Michael Love
41k • written 2.5 years ago by
oliver.ziff
• 0
0
votes
2
replies
941
views
Design formula in DESeq2
model
BatchEffect
hidden
Design
DESeq2
2.5 years ago
m.glymenaki
• 0
2
votes
3
replies
1.3k
views
Contrast treated samples against both scramble and untreated controls
design
contrast
DESeq2
updated 2.5 years ago by
Michael Love
41k • written 2.5 years ago by
oliver.ziff
• 0
0
votes
1
reply
1.7k
views
DESeq2 time course and dosage response
LRT
Design
DESeq2
doseResponse
TimeSeriesExperiment
updated 2.7 years ago by
Michael Love
41k • written 2.7 years ago by
Mari
• 0
0
votes
1
reply
952
views
Subject paired DESeq2 design
DESeq2
paired
design
updated 2.7 years ago by
Michael Love
41k • written 2.7 years ago by
dr
▴ 10
0
votes
1
reply
695
views
[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2
nesting
design
updated 2.8 years ago by
Michael Love
41k • written 2.8 years ago by
christophe.vanhaver
• 0
2
votes
5
replies
3.2k
views
DESeq2 with two continuous variable in a design
DESeq2
RNASeq
R
design
updated 18 months ago by
Michael Love
41k • written 2.8 years ago by
sofia
• 0
2
votes
3
replies
1.2k
views
Differential expression error in edgeR - maybe from design matrix?
design
edgeR
matrix
RNA-seq
MDplot
updated 2.9 years ago by
Gordon Smyth
50k • written 2.9 years ago by
Alex
• 0
2
votes
3
replies
7.5k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions
DESeq2
Design
updated 3.3 years ago by
Kevin Blighe
★ 3.9k • written 3.3 years ago by
vanbelj
▴ 30
0
votes
1
reply
754
views
DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2
design
formula
updated 3.5 years ago by
Michael Love
41k • written 3.5 years ago by
Bine
▴ 40
2
votes
3
replies
836
views
EdgeR design matrix for mutlifactor RNA seq
edger
design
multifactor
updated 3.5 years ago by
James W. MacDonald
65k • written 3.5 years ago by
jackiesalzbank
• 0
0
votes
5
replies
1.6k
views
DESeq2 issue with hierarchical clustering
deseq2
design
updated 3.6 years ago by
Kevin Blighe
★ 3.9k • written 3.6 years ago by
mhnidhi2-c
• 0
2
votes
5
replies
1.1k
views
Picking the right design formula
deseq2
design
experiment
3.6 years ago
donnenfieldjonah
• 0
4
votes
5
replies
2.9k
views
How to incorporate batch effect that is only present in one level into the design?
linear model
batch effect
DESeq2
design
updated 3.7 years ago by
James W. MacDonald
65k • written 3.7 years ago by
tim.meese
• 0
2
votes
8
replies
4.2k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma
deseq2
batch
design
batch effect
3.7 years ago
Pietro
▴ 40
4
votes
7
replies
1.1k
views
Genes upregulated in one condition vs each of the other conditions
edger
design
updated 3.8 years ago by
Gordon Smyth
50k • written 3.8 years ago by
dario.beraldi
• 0
0
votes
1
reply
801
views
Coefficients not estimable voom Lima with multiple numeric covariate
r
limma
design
rnaseq
voom
updated 3.9 years ago by
Gordon Smyth
50k • written 3.9 years ago by
Will
• 0
2
votes
7
replies
2.0k
views
Limma analysis with multiple variables
limma
model.matrix
de
design
rnaseq
updated 3.9 years ago by
Gordon Smyth
50k • written 3.9 years ago by
Will
• 0
6
votes
6
replies
1.2k
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq
design
linear model
glm
updated 4.2 years ago by
Steve Lianoglou
★ 13k • written 4.2 years ago by
tmms
• 0
0
votes
10
replies
2.4k
views
DEseq2 design formula correcting for batch
deseq2
design
formula
batch effect
updated 4.2 years ago by
swbarnes2
★ 1.3k • written 4.2 years ago by
l.rijnberk
• 0
1
vote
4
replies
821
views
Help with Deseq2 design
deseq2
design
multifactor
updated 4.3 years ago by
Michael Love
41k • written 4.3 years ago by
sxp585
• 0
1
vote
1
reply
25k
views
lfcShrink doesn't work with contrasts
lfcShrink
contrast
design
deseq2
updated 4.3 years ago by
Michael Love
41k • written 4.3 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
971
views
Design of time-course experiment in DESeq2
deseq2
design
design formula
time course
lrt
updated 4.3 years ago by
Michael Love
41k • written 4.3 years ago by
ac_bioinformatics
• 0
2
votes
1
reply
1.3k
views
combining columns for experimental design in DESeq2
deseq2
design
metadata
updated 4.3 years ago by
sebastian.lobentanzer
▴ 50 • written 4.3 years ago by
Assa Yeroslaviz
★ 1.5k
1
vote
8
replies
7.2k
views
DESeq2: Continuous and discreate variables in the design
deseq2
R
rna-seq
design
updated 3.3 years ago by
Michael Love
41k • written 4.4 years ago by
raquelgarza95
• 0
1
vote
6
replies
1.5k
views
Relations between average expression and fold change
design
AveExpr
comparisons
updated 4.5 years ago by
James W. MacDonald
65k • written 4.5 years ago by
Lluís Revilla Sancho
▴ 730
0
votes
1
reply
1.4k
views
DESeq2 comparison of treatment within tissue type, ignoring other tissue type
deseq2
comparison
design
paired
treatment
updated 4.5 years ago by
swbarnes2
★ 1.3k • written 4.5 years ago by
tinglec
• 0
0
votes
4
replies
1.7k
views
DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2
contrast
design
4.6 years ago
luciest.rodriguez
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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