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Showing :
design matrix
•
reset
3
votes
4
replies
5.0k
views
multiple comparison using limma
limma
design matrix
makecontrasts
multiple comparisons
7.3 years ago
annabelle.congras
▴ 10
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
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
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
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
2.1k
views
Design matrix for unbalanced data
edgeR
RNA-Seq
design matrix
multifactorial design
8.2 years ago
Yogender Gowtham
▴ 20
0
votes
2
replies
888
views
Anyone see whats causing EdgeR to report Design matrix not of full rank.?
edger
design matrix
8.2 years ago
nickschurch
• 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
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
0
votes
2
replies
1.5k
views
stimulation effects between wild-type and knockout cells using deseq
multiple factor design
interactions
design matrix
deseq2
updated 6.5 years ago by
Michael Love
42k • written 8.5 years ago by
Assa Yeroslaviz
★ 1.5k
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
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
0
votes
2
replies
755
views
Limma design matrix
limma
design matrix
updated 6.0 years ago by
Gordon Smyth
50k • written 6.0 years ago by
R
▴ 40
0
votes
2
replies
778
views
Differential Expression Analysis on a Subset Derived from a Previous Contrast in edgeR or DESeq2
deseq2
design formula
design matrix
edgeR
ATAC
updated 4.4 years ago by
Gordon Smyth
50k • written 4.4 years ago by
corinne_hutfilz
• 0
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
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
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
1
vote
4
replies
834
views
EdgeR multiple factor design question
edger
design matrix
7.5 years ago
bioinformatics
▴ 10
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
0
votes
3
replies
703
views
Proper Design Matrix for Paired Samples where endpoint has multiple samples that pair to the same start sample
edger
design matrix
updated 8.0 years ago by
Aaron Lun
★ 28k • written 8.0 years ago by
laura
• 0
1
vote
3
replies
930
views
Defining the design matrix
design matrix
7.8 years ago
humberto_munoz
• 0
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
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
1
vote
17
replies
1.8k
views
design for edgeR
edger
design matrix
glmlrt
updated 7.4 years ago by
Aaron Lun
★ 28k • written 7.4 years ago by
simarsidhu25
• 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
0
votes
8
replies
3.9k
views
Design question limma multi variables
limma
design matrix
updated 7.3 years ago by
Aaron Lun
★ 28k • written 7.3 years ago by
Stane
▴ 40
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
0
votes
7
replies
2.4k
views
DESeq2: how to identify confounding variable in the design matrix
deseq2
confounders
design matrix
rnaseq
7.1 years ago
lina.faller
▴ 10
0
votes
1
reply
1.3k
views
Test for differential variability with missMethyl (DiffVar) using block design
missmethyl
diffvar
design matrix
limma
block
updated 6.0 years ago by
lhuang7
▴ 50 • written 6.9 years ago by
Simone
▴ 190
0
votes
2
replies
3.0k
views
Time-course analysis with limma for >3 time points
limma
contrast matrix
design matrix
multiple time points
timecourse
updated 3.0 years ago by
rf
• 0 • written 6.9 years ago by
relathman
▴ 20
1
vote
2
replies
1.1k
views
DESeq2 design matrix with a single mock and multiple timepoints
deseq2
design matrix
updated 6.7 years ago by
Michael Love
42k • written 6.7 years ago by
ap3637
• 0
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
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
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
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
0
votes
4
replies
1.6k
views
edgeR design matrix
edgeR
design and contrast matrix
design matrix
updated 6.2 years ago by
Gordon Smyth
50k • written 6.2 years ago by
cafelumiere12
▴ 20
0
votes
5
replies
1.1k
views
differential expression analysis of cell subtypes mixture
deseq2
edgeR
design matrix
multifactorial design
updated 6.2 years ago by
Aaron Lun
★ 28k • written 6.2 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
1.0k
views
DESeq account for using two different siRNA constructs to knockdown same gene
deseq2
design and contrast matrix
multiple factor design
design matrix
updated 6.1 years ago by
Michael Love
42k • written 6.1 years ago by
khhsource
• 0
0
votes
1
reply
735
views
RNAseq DESeq2 paired data design help
rnaseq
design matrix
deseq2
updated 6.1 years ago by
Michael Love
42k • written 6.1 years ago by
umlch
• 0
1
vote
2
replies
7.5k
views
DESEQ2 design with multiple conditions
deseq2
design matrix
updated 6.1 years ago by
Michael Love
42k • written 6.1 years ago by
vrehaman
• 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
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
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
0
votes
1
reply
1.0k
views
Creating a design matrix
design matrix
limma
updated 5.5 years ago by
Gordon Smyth
50k • written 5.7 years ago by
mahm
▴ 20
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
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
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
0
votes
11
replies
3.2k
views
Limma Design Matrix for Paired Samples with Confouding Factors
limma
design matrix
paired samples
confounding factors
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
yuabrahamliu
• 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
820
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
50 results • Page
1 of 1
Recent ...
Replies
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…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
Ken C
• 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
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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