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design matrix
•
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3
votes
7
replies
1.6k
views
single continuous factor
edger
design matrix
continuous
updated 2.2 years ago by
Tongjun
• 0 • written 6.0 years ago by
ashley.lu
• 0
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
0
votes
3
replies
894
views
DESeq2 accounting for two confounders with interaction in the design matrix
deseq2
design matrix
multi-confounders
linear models
rna-seq
updated 4.2 years ago by
Michael Love
42k • written 4.2 years ago by
mohamedrefaat.1.1992
• 0
0
votes
2
replies
774
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
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
0
votes
2
replies
623
views
DESeq2 design matrix choice
deseq2
design matrix
updated 4.7 years ago by
Michael Love
42k • written 4.7 years ago by
Yang WY
• 0
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
1
vote
5
replies
951
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
0
votes
1
reply
774
views
DESeq2, how to deal with batch effect: t-test or design matrix?
deseq2
batch
sva
t-test
design matrix
updated 5.0 years ago by
Michael Love
42k • written 5.0 years ago by
Mozart
▴ 30
0
votes
0
replies
717
views
Paired DE analysis in edgeR with trios of samples while blocking for various confounders
edger
rnaseq
paired analysis
design matrix
5.1 years ago
svlachavas
▴ 830
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
0
votes
1
reply
739
views
differentail expression analysis with interaction terms
edger
deseq2
interaction
design matrix
updated 5.2 years ago by
James W. MacDonald
65k • written 5.2 years ago by
Assa Yeroslaviz
★ 1.5k
2
votes
2
replies
835
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
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
5.3 years ago
nikosbosse
• 0
0
votes
5
replies
1.7k
views
DESeq2 package : Error in checkFullRank(modelMatrix) while designing multi factor
DESeq2
multiple factor design
design model
design matrix
rna-seq
updated 5.4 years ago by
Michael Love
42k • written 5.4 years ago by
iammiso
• 0
2
votes
2
replies
814
views
DESeq results gives all genes
deseq2
design matrix
results
updated 5.4 years ago by
Michael Love
42k • written 5.4 years ago by
evocanres
• 0
2
votes
1
reply
913
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
1.3k
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
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
0
votes
11
replies
3.2k
views
Limma Design Matrix for Paired Samples with Confouding Factors
limma
design matrix
paired samples
confounding factors
updated 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
yuabrahamliu
• 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
2
votes
1
reply
622
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
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
3
replies
1.3k
views
Design Matrix with paired and independent samples plus RUVg Spike-in normalization
edger
design matrix
paired samples
ruvseq
updated 5.7 years ago by
James W. MacDonald
65k • written 5.7 years ago by
ChrisM
• 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
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
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 5.8 years ago by
Gordon Smyth
50k • written 5.8 years ago by
reubenmcgregor88
• 0
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
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
0
votes
2
replies
752
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
1
reply
730
views
RNAseq DESeq2 paired data design help
rnaseq
design matrix
deseq2
updated 6.0 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 6.0 years ago by
Michael Love
42k • written 6.0 years ago by
vrehaman
• 0
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
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
0
votes
5
replies
1.1k
views
differential expression analysis of cell subtypes mixture
deseq2
edgeR
design matrix
multifactorial design
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
4
replies
1.6k
views
edgeR design matrix
edgeR
design and contrast matrix
design matrix
updated 6.1 years ago by
Gordon Smyth
50k • written 6.2 years ago by
cafelumiere12
▴ 20
1
vote
4
replies
947
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
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
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
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
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
7
replies
2.0k
views
complex design for chip-seq analysis
chipseq
csaw
limma
design matrix
multiple factor design
updated 6.5 years ago by
Aaron Lun
★ 28k • written 6.5 years ago by
Assa Yeroslaviz
★ 1.5k
6
votes
3
replies
6.9k
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
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
0
votes
0
replies
1.1k
views
Possible confounding of variable of interest with batch covariate and Partial NA coefficients when including batch in limma linear model for microarr…
limma
batch effect
design matrix
microarray
confounding
7.0 years ago
svlachavas
▴ 830
0
votes
7
replies
2.4k
views
DESeq2: how to identify confounding variable in the design matrix
deseq2
confounders
design matrix
rnaseq
7.0 years ago
lina.faller
▴ 10
3
votes
4
replies
4.9k
views
multiple comparison using limma
limma
design matrix
makecontrasts
multiple comparisons
7.3 years ago • updated 7.2 years ago
annabelle.congras
▴ 10
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
2
votes
6
replies
3.3k
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
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
50 results • Page
1 of 1
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Replies
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results
by
swbarnes2
★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Mike Smith
★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
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by
Ian D.
▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Comment: Extremely small p-values using Limma for proteomic data
by
Robert Castelo
★ 3.3k
From the point of view of visualization, I find handy the fact that raw p-values give more resolution than adjusted ones, which allows one …
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
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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