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design
•
reset
6
votes
6
replies
2.8k
views
design matrix for 4 groups in edgeR
edger
design
9.5 years ago
alakatos
▴ 130
4
votes
18
replies
24k
views
DEseq2 time-series design.
deseq2
timecourse
design
updated 4.8 years ago by
simon baldwin
• 0 • written 9.5 years ago by
shao
▴ 100
2
votes
8
replies
2.4k
views
DESeq design question
deseq2
design
9.5 years ago • updated 9.1 years ago
sunkid
• 0
4
votes
13
replies
2.5k
views
Which formula should I use to set the best model matrix for my analysis ?
DESEQ2
EDGER
design
7.6 years ago
ZheFrench
▴ 50
3
votes
13
replies
2.2k
views
Design and independent filtering of patient RNA-seq data
differential gene expression
deseq2
design
independent filtering
limma
updated 8.9 years ago by
James W. MacDonald
65k • written 8.9 years ago by
mat.lesche
▴ 90
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
0
votes
3
replies
827
views
Analysis strategy - possible to use naive control group as t=0 for two treatment groups?
Deseq2
design
time course
basal group
updated 4.8 years ago by
Michael Love
41k • written 4.8 years ago by
Rob Buurstede
• 0
0
votes
8
replies
1.9k
views
Two controls in RNAseq formula for DESeq2
deseq2
formula
controls
design
updated 4.7 years ago by
Michael Love
41k • written 4.7 years ago by
taveluz
• 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
6
replies
188
views
Once again a "Model matrix not full rank"
DESeq2
design
coldata
updated 1 day ago by
swbarnes2
★ 1.3k • written 3 days ago by
arfranco
▴ 130
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 2.9 years ago by
sofia
• 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
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
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
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
0
votes
5
replies
1.0k
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
5
replies
1.4k
views
DESeq2 It is correct to use interaction term for patient variability?
deseq2
design
interaction term
R
6.2 years ago
briverog
• 0
2
votes
4
replies
924
views
Limma model for paired and pool together
limma
design
rnaseq
updated 6.1 years ago by
Ryan C. Thompson
★ 7.9k • written 6.1 years ago by
b.nota
▴ 360
0
votes
5
replies
1.3k
views
DESeq2 design formula - correlation with ordered variable
DESeq2
design
formula
matrix
updated 5.9 years ago by
Michael Love
41k • written 5.9 years ago by
t.kuilman
▴ 170
5
votes
6
replies
1.6k
views
How to set up appropriate analysis using sample type and condition for DESeq2
deseq2
differential gene expression
design
updated 5.6 years ago by
Michael Love
41k • written 5.6 years ago by
newbio17
• 0
0
votes
7
replies
1.3k
views
DeSeq2 Ribosome Profiling: multiple factor design
deseq2
design
timeseries
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
indrik.wijaya
▴ 20
3
votes
6
replies
2.7k
views
Limma design/contrast correct?
limma
microarray
design
paired
mixed model
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
rasmus.agren
• 0
0
votes
2
replies
1.7k
views
DESeq2- multifactor design- 3 conditions and 3 timepoints
deseq2
design
updated 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
bioinfo
• 0
0
votes
1
reply
589
views
DESeq2 3 factor design - whether to split up data or add interaction terms
deseq2
design
updated 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
atongz652
• 0
0
votes
7
replies
1.5k
views
Problems with DESeq2 'design' parameter using Shiny/rhandsontable
deseq2
shiny
design
rhandsontable
hot_to_r()
updated 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
hinkel2
• 0
3
votes
4
replies
1.3k
views
Paired analysis (tumor vs normal) at three different conditions with EdgeR
edger
design
matrix
de
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
takumima
▴ 10
3
votes
5
replies
1.4k
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
Pietro
▴ 40
3
votes
3
replies
788
views
Extracting within subject effect in a between and within subject model with DESeq2
deseq2
design
updated 5.1 years ago by
Michael Love
41k • written 5.1 years ago by
i.sudbery
▴ 40
0
votes
1
reply
623
views
Perform time course rna seq analysis at once with a single design or separate differential analysis for each time point
deseq2
design
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
adhikb
• 0
1
vote
1
reply
999
views
All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2
differential expression
batch correction
design
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
wunderl
▴ 40
0
votes
1
reply
637
views
DESeq2 analysis of multifactorial RNAseq experiment
deseq2
design
time-course
updated 4.9 years ago by
Michael Love
41k • written 4.9 years ago by
Victor Chano
• 0
0
votes
1
reply
1.5k
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
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
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
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
0
votes
2
replies
972
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
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
1
vote
4
replies
822
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
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
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
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
0
votes
1
reply
803
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
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
2
votes
5
replies
1.1k
views
Picking the right design formula
deseq2
design
experiment
3.6 years ago
donnenfieldjonah
• 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
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
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
0
votes
2
replies
942
views
Design formula in DESeq2
model
BatchEffect
hidden
Design
DESeq2
2.5 years ago
m.glymenaki
• 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 3.4 years ago by
vanbelj
▴ 30
0
votes
2
replies
685
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
50 results • Page
1 of 1
Recent ...
Replies
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Intent to delete when going home. Sorry for that!
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
Please ask you own question. Inserting your own dataset into someone else's question like this is very impolite. I have already answered m…
Comment: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
limma most certainly is available. It installs in R 4.4.0 and Bioc 3.19 for all platforms without any issues. It has not had any period of …
Comment: package goseq seems to be not available on the latest version of R
by
Patrycja
▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Chris
• 0
Thanks Gordon for the advice!
Votes
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
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