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design matrix
•
reset
18
votes
37
replies
17k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma
illumina
differential gene expression
multiple comparisons
design matrix
9.0 years ago • updated 8.8 years ago
svlachavas
▴ 830
11
votes
14
replies
4.3k
views
Setting up the Design Matrix
rnaseq
edgeR
multiple factor design
design matrix
8.3 years ago
Yogender Gowtham
▴ 20
7
votes
5
replies
1.6k
views
Which is the best design matrix to compare a timecourse between two conditions?
limma
voom
design matrix
timecourse
updated 7.3 years ago by
Gordon Smyth
50k • written 7.3 years ago by
Camila Orellana
▴ 10
7
votes
11
replies
3.3k
views
Continuous variable interaction with Groups in design matrix
edger
design matrix
updated 8.3 years ago by
Aaron Lun
★ 28k • written 8.3 years ago by
jhj89
▴ 10
6
votes
3
replies
7.0k
views
deseq2 correcting for batch effects
deseq2
batch effect
removebatcheffect()
design matrix
updated 6.6 years ago by
Michael Love
42k • written 6.6 years ago by
Assa Yeroslaviz
★ 1.5k
6
votes
4
replies
2.6k
views
discrepance in DESeq2 results with different design structures
deseq2
differential expression
independent filtering
pre-filtering
design matrix
9.1 years ago
Assa Yeroslaviz
★ 1.5k
5
votes
12
replies
2.0k
views
how to use edgeR analysis RNA-seq data which has four factors
edger
design matrix
comparing more than two groups
multiple factor design
8.3 years ago • updated 8.1 years ago
xiaoaozqd
• 0
5
votes
5
replies
1.4k
views
Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
limma
design and contrast matrix
design matrix
contrast matrix
updated 5.6 years ago by
James W. MacDonald
65k • written 5.6 years ago by
mikhael.manurung
▴ 270
5
votes
2
replies
1.9k
views
DESeq2 batch effect with and without interaction model
deseq2
rna-seq
R
linear model
design matrix
updated 6.5 years ago by
Michael Love
42k • written 6.5 years ago by
gdagstn
▴ 10
5
votes
7
replies
3.6k
views
Deseq2 design for one condition over 8 different time point
deseq2
rna-seq
design matrix
deseq
updated 5.6 years ago by
Michael Love
42k • written 5.6 years ago by
thindmarsmission
▴ 10
4
votes
3
replies
1.3k
views
What is the correct contrast matrix if one treatment must be compared to both of the other two treatments, but separately?
edger
limma
model.matrix
contrast matrix
design matrix
updated 7.8 years ago by
Gavin Kelly
▴ 680 • written 7.8 years ago by
Peter
• 0
4
votes
4
replies
1.7k
views
edgeR: How can I determine which factors significantly explain my DE genes?
edger
differential gene expression
model.matrix
design matrix
updated 6.0 years ago by
Gordon Smyth
50k • written 6.0 years ago by
Robert Gilmore
• 0
4
votes
4
replies
1.8k
views
Is this design matrix correct (treament factor with three levels)?
edger
limma
design matrix
8.3 years ago
Ekarl2
▴ 80
4
votes
8
replies
2.5k
views
Can't find any differentially expressed genes
rnaseq
differential gene expression
design matrix
edgeR
updated 9.1 years ago by
Gordon Smyth
50k • written 9.1 years ago by
s3462450
▴ 10
4
votes
7
replies
1.1k
views
Design matrix and contrast for RNA knockdown experiment
design matrix
limma
contrast matrix
updated 7.6 years ago by
Aaron Lun
★ 28k • written 7.6 years ago by
maltethodberg
▴ 180
4
votes
9
replies
1.2k
views
Statistical background for computing intial estimates for the means of negative binomially distributed gene counts in DESeq2
deseq2
design matrix
5.4 years ago
nikosbosse
• 0
3
votes
7
replies
2.0k
views
complex design for chip-seq analysis
chipseq
csaw
limma
design matrix
multiple factor design
updated 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
Assa Yeroslaviz
★ 1.5k
3
votes
1
reply
1.6k
views
using variable in design formula
deseq2
r
design matrix
updated 7.7 years ago by
Michael Love
42k • written 7.7 years ago by
igor
▴ 50
3
votes
6
replies
1.7k
views
Design that evaluates response to continuous and categorical variables
limma
design and contrast matrix
design matrix
limma design matrix
updated 8.9 years ago by
James W. MacDonald
65k • written 8.9 years ago by
Moritz E. Beber
▴ 10
3
votes
7
replies
1.6k
views
single continuous factor
edger
design matrix
continuous
updated 2.3 years ago by
Tongjun
• 0 • written 6.0 years ago by
ashley.lu
• 0
3
votes
6
replies
1.0k
views
Overlapping treatments in the design matrix
edger
design matrix
updated 8.3 years ago by
Aaron Lun
★ 28k • written 8.3 years ago by
jhj89
▴ 10
3
votes
4
replies
5.0k
views
multiple comparison using limma
limma
design matrix
makecontrasts
multiple comparisons
7.3 years ago
annabelle.congras
▴ 10
3
votes
6
replies
1.3k
views
EdgeR model formula design matrix
edger
design matrix
paired samples
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
aiko
• 0
3
votes
12
replies
2.8k
views
Questions about complex design in limma regarding an agilent microarray dataset with multiple time points and different biological replicates
limma
design matrix
multiple time points
agilent microarrays
updated 8.2 years ago by
Aaron Lun
★ 28k • written 8.2 years ago by
Konstantinos Yeles
▴ 80
3
votes
8
replies
1.3k
views
Design matrix for a two-color experimental design testing for time effect on 3 treated cell-lines, each with its own time=0 control
limma
microarray
design matrix
twochannel
updated 5.8 years ago by
Gordon Smyth
50k • written 5.8 years ago by
rubi
▴ 110
2
votes
1
reply
1.1k
views
Limma Design matrix for time series+treatment+batch effect
limma
factorial
design matrix
microarray
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
senthil.duraikannukailasam
• 0
2
votes
3
replies
1.3k
views
Design Matrix with paired and independent samples plus RUVg Spike-in normalization
edger
design matrix
paired samples
ruvseq
updated 5.8 years ago by
James W. MacDonald
65k • written 5.8 years ago by
ChrisM
• 0
2
votes
1
reply
624
views
edgeR with related individuals?
edgeR
related
design matrix
updated 5.6 years ago by
James W. MacDonald
65k • written 5.6 years ago by
joanna.l.kelley
• 0
2
votes
2
replies
1.4k
views
EdgeR User Guide: use of glmLRT vs glmQLF in oral carcinoma Case Study
edger
design matrix
glmlrt()
glmQFTest()
paired design
5.5 years ago
oakhamwolf
• 0
2
votes
1
reply
918
views
EdgeR: With two treatments, is it equivalent to split into two different models vs. making the relevant pairwise comparisons?
edgeR
design matrix
contrast
updated 5.5 years ago by
Gordon Smyth
50k • written 5.5 years ago by
sdalin
• 0
2
votes
2
replies
821
views
DESeq results gives all genes
deseq2
design matrix
results
updated 5.5 years ago by
Michael Love
42k • written 5.5 years ago by
evocanres
• 0
2
votes
2
replies
841
views
Limma design matrix separate channel analysis with same control
limma
design matrix
gene expression
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
Guillaume Robert
• 0
2
votes
10
replies
2.8k
views
Time-series analysis with DESeq2
deseq2
time-series
design matrix
edger
updated 5.2 years ago by
Michael Love
42k • written 5.2 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
13
replies
1.9k
views
problem about (design matrix)
limma
limma design matrix
design matrix
updated 8.3 years ago by
Aaron Lun
★ 28k • written 8.3 years ago by
libya.tahani
• 0
2
votes
10
replies
2.1k
views
Design matrix for unbalanced data
edgeR
RNA-Seq
design matrix
multifactorial design
8.2 years ago
Yogender Gowtham
▴ 20
2
votes
5
replies
849
views
a complicate scenario for Design Matrix
edgeR
design matrix
updated 8.1 years ago by
Aaron Lun
★ 28k • written 8.1 years ago by
kainblue100
• 0
2
votes
2
replies
1.3k
views
DESeq2 multifactorial design with unpaired individuals
deseq2
design matrix
updated 7.3 years ago by
Michael Love
42k • written 7.3 years ago by
fanli.gcb
• 0
2
votes
5
replies
3.8k
views
design model matrix for nested factors (edgeR)
edger
design matrix
model matrix
updated 9.1 years ago by
Aaron Lun
★ 28k • written 9.1 years ago by
silvia.paolucci81
• 0
2
votes
6
replies
3.4k
views
RNA-seq paired analysis design
paired samples
design matrix
limma
deseq2
edger
updated 7.3 years ago by
Gordon Smyth
50k • written 7.3 years ago by
cjmb3
• 0
2
votes
4
replies
8.6k
views
Limma LmFit() giving error: Error in lm.fit(design, t(M)) : incompatible dimension
limma
differential expression
design matrix
error
eset
updated 8.9 years ago by
Aaron Lun
★ 28k • written 8.9 years ago by
Vani
▴ 20
2
votes
13
replies
2.1k
views
LIMMA : group specific effect of a treatment while controlling for individual effect
limma-voom
design matrix
limma time-course
limma design matrix
limma
6.2 years ago
SPbeginner
• 0
2
votes
10
replies
1.8k
views
Am I on the right tracks with a 3 factor design in Limma?
r
limma
design matrix
biobase
updated 5.9 years ago by
Gordon Smyth
50k • written 5.9 years ago by
reubenmcgregor88
• 0
2
votes
8
replies
3.8k
views
EdgeR. Analysis with pairing across condition and treatment. Design Matrix
edger
ANOVA
Design matrix
updated 9.3 years ago by
Gordon Smyth
50k • written 9.3 years ago by
chwhite
• 0
2
votes
2
replies
2.4k
views
DMRcate cpg.annotate error
dmrcate
design matrix
updated 8.5 years ago by
Tim Peters
▴ 180 • written 8.5 years ago by
Giovanni Calice
▴ 160
1
vote
1
reply
2.5k
views
EdgeR:Calculating differential expression within/between groups in nested designs
edger
nested
design matrix
differential expression
updated 9.2 years ago by
Aaron Lun
★ 28k • written 9.2 years ago by
Mauve
• 0
1
vote
4
replies
1.6k
views
edgeR design matrix for 2 variables + batch effect
egdeR
design matrix
batch effect
updated 4.5 years ago by
Gordon Smyth
50k • written 4.5 years ago by
ahsindoomilup
• 0
1
vote
18
replies
2.0k
views
Microarray expression analysis for on factor taking account confounders (covariables)
limma
design matrix
matrix with covariables
updated 6.2 years ago by
Aaron Lun
★ 28k • written 6.2 years ago by
michel655
• 0
1
vote
8
replies
1.6k
views
Design matrix for regressing gene expression on a continuous variable - age
limma
lmfit
design matrix
r
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
anupriya.dalmia
• 0
1
vote
4
replies
954
views
Deseq multifactor test design full rank error and how to determine one variable only effect.
deseq2
multiple factor design
design matrix
6.2 years ago
jaime.alvarez.benayas
• 0
1
vote
5
replies
971
views
DESEQ2 design matrix for double knockout interaction with condition
deseq2
model.matrix
design matrix
updated 5.0 years ago by
Michael Love
42k • written 5.0 years ago by
user9635643
• 0
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
jane
• 0
Your material was totally correct, therefore I was able to learn what I needed to know. I'd want to convey my heartfelt gratitude for shari…
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
Galina
• 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error
by
ATpoint
★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
robersy
• 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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