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Showing :
Design
•
reset
2
votes
2
replies
107
views
Handling NA values in limma's voom design matrix
limma
voom
design
NAs
updated 14 days ago by
Gordon Smyth
45k • written 14 days ago by
dr
▴ 10
0
votes
4
replies
221
views
DESeq2 pseudotime series design?
DESeq2
design
12 weeks ago • updated 11 weeks ago
jordi.planells
• 0
0
votes
2
replies
200
views
DeSeq2 - design formula for enrichment on combinated conditions AB, not A, not B
conditions
design
DESeq2
Synergy
updated 5 months ago by
Michael Love
37k • written 5 months ago by
johannesdolberg
• 0
0
votes
1
reply
192
views
Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast
design
DESeq2
continuous
updated 5 months ago by
Michael Love
37k • written 5 months ago by
tiansy
• 0
1
vote
1
reply
238
views
Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment
RNASeq
design
DESeq2
updated 5 months ago by
Michael Love
37k • written 5 months ago by
Kesava
• 0
1
vote
2
replies
280
views
Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq
Design
Matrix
6 months ago
Barista
• 0
0
votes
2
replies
375
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions
design
Multifactorial
DESeq2
updated 6 months ago by
swbarnes2
★ 1.0k • written 6 months ago by
Marie
• 0
0
votes
1
reply
167
views
Account for parent cell line when comparing isogenic mutants
interactions
design
DESeq2
updated 6 months ago by
Michael Love
37k • written 6 months ago by
oliver.ziff
• 0
0
votes
2
replies
243
views
Design formula in DESeq2
model
BatchEffect
hidden
Design
DESeq2
6 months ago
m.glymenaki
• 0
2
votes
3
replies
342
views
Contrast treated samples against both scramble and untreated controls
design
contrast
DESeq2
updated 7 months ago by
Michael Love
37k • written 7 months ago by
oliver.ziff
• 0
0
votes
1
reply
419
views
DESeq2 time course and dosage response
LRT
Design
DESeq2
doseResponse
TimeSeriesExperiment
updated 9 months ago by
Michael Love
37k • written 9 months ago by
Mari
• 0
0
votes
1
reply
210
views
Subject paired DESeq2 design
DESeq2
paired
design
updated 9 months ago by
Michael Love
37k • written 9 months ago by
dr
▴ 10
0
votes
1
reply
277
views
[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2
nesting
design
updated 10 months ago by
Michael Love
37k • written 10 months ago by
christophe.vanhaver
• 0
2
votes
3
replies
748
views
DESeq2 with two continuous variable in a design
DESeq2
RNASeq
R
design
updated 10 months ago by
Michael Love
37k • written 11 months ago by
sofia
• 0
2
votes
3
replies
475
views
Differential expression error in edgeR - maybe from design matrix?
design
edgeR
matrix
RNA-seq
MDplot
updated 12 months ago by
Gordon Smyth
45k • written 12 months ago by
Alex
• 0
2
votes
3
replies
1.5k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions
DESeq2
Design
updated 16 months ago by
Kevin Blighe
3.5k • written 17 months ago by
vanbelj
▴ 10
0
votes
1
reply
224
views
DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2
design
formula
updated 19 months ago by
Michael Love
37k • written 19 months ago by
Bine
▴ 20
2
votes
3
replies
351
views
EdgeR design matrix for mutlifactor RNA seq
edger
design
multifactor
updated 19 months ago by
James W. MacDonald
60k • written 19 months ago by
jackiesalzbank
• 0
0
votes
5
replies
427
views
DESeq2 issue with hierarchical clustering
deseq2
design
updated 20 months ago by
Kevin Blighe
3.5k • written 20 months ago by
mhnidhi2-c
• 0
2
votes
5
replies
419
views
Picking the right design formula
deseq2
design
experiment
20 months ago
donnenfieldjonah
• 0
2
votes
5
replies
1.1k
views
How to incorporate batch effect that is only present in one level into the design?
linear model
batch effect
DESeq2
design
updated 21 months ago by
James W. MacDonald
60k • written 21 months ago by
tim.meese
• 0
2
votes
8
replies
1.7k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma
deseq2
batch
design
batch effect
21 months ago
Pietro
▴ 30
4
votes
7
replies
365
views
Genes upregulated in one condition vs each of the other conditions
edger
design
updated 22 months ago by
Gordon Smyth
45k • written 22 months ago by
dario.beraldi
• 0
0
votes
1
reply
286
views
Coefficients not estimable voom Lima with multiple numeric covariate
r
limma
design
rnaseq
voom
updated 23 months ago by
Gordon Smyth
45k • written 23 months ago by
Will
• 0
2
votes
7
replies
624
views
Limma analysis with multiple variables
limma
model.matrix
de
design
rnaseq
updated 23 months ago by
Gordon Smyth
45k • written 23 months ago by
Will
• 0
6
votes
6
replies
445
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq
design
linear model
glm
updated 2.3 years ago by
Steve Lianoglou
13k • written 2.3 years ago by
tmms
• 0
0
votes
10
replies
634
views
DEseq2 design formula correcting for batch
deseq2
design
formula
batch effect
updated 2.3 years ago by
swbarnes2
★ 1.0k • written 2.3 years ago by
l.rijnberk
• 0
1
vote
4
replies
319
views
Help with Deseq2 design
deseq2
design
multifactor
updated 2.3 years ago by
Michael Love
37k • written 2.3 years ago by
sxp585
• 0
1
vote
1
reply
13k
views
lfcShrink doesn't work with contrasts
lfcShrink
contrast
design
deseq2
updated 2.4 years ago by
Michael Love
37k • written 2.4 years ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
306
views
Design of time-course experiment in DESeq2
deseq2
design
design formula
time course
lrt
updated 2.4 years ago by
Michael Love
37k • written 2.4 years ago by
ac_bioinformatics
• 0
2
votes
1
reply
264
views
combining columns for experimental design in DESeq2
deseq2
design
metadata
updated 2.4 years ago by
sebastian.lobentanzer
▴ 50 • written 2.4 years ago by
Assa Yeroslaviz
★ 1.5k
1
vote
8
replies
2.8k
views
DESeq2: Continuous and discreate variables in the design
deseq2
R
rna-seq
design
updated 17 months ago by
Michael Love
37k • written 2.5 years ago by
raquelgarza95
• 0
1
vote
6
replies
522
views
Relations between average expression and fold change
design
AveExpr
comparisons
updated 2.5 years ago by
James W. MacDonald
60k • written 2.5 years ago by
Lluís Revilla Sancho
▴ 660
0
votes
1
reply
681
views
DESeq2 comparison of treatment within tissue type, ignoring other tissue type
deseq2
comparison
design
paired
treatment
updated 2.5 years ago by
swbarnes2
★ 1.0k • written 2.5 years ago by
tinglec
• 0
0
votes
4
replies
958
views
DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2
contrast
design
2.6 years ago
luciest.rodriguez
• 0
0
votes
2
replies
378
views
different designs for finding DEG by limma
limma
DEG
design
2.7 years ago
amin.ghareyazi
• 0
0
votes
8
replies
707
views
Two controls in RNAseq formula for DESeq2
deseq2
formula
controls
design
updated 2.8 years ago by
Michael Love
37k • written 2.8 years ago by
taveluz
• 0
0
votes
3
replies
355
views
Analysis strategy - possible to use naive control group as t=0 for two treatment groups?
Deseq2
design
time course
basal group
updated 2.9 years ago by
Michael Love
37k • written 2.9 years ago by
Rob Buurstede
• 0
2
votes
18
replies
18k
views
DEseq2 time-series design.
deseq2
timecourse
design
updated 2.9 years ago by
simon baldwin
• 0 • written 7.6 years ago by
shao
▴ 90
0
votes
1
reply
324
views
DESeq2 analysis of multifactorial RNAseq experiment
deseq2
design
time-course
updated 2.9 years ago by
Michael Love
37k • written 2.9 years ago by
Victor Chano
• 0
1
vote
1
reply
455
views
All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2
differential expression
batch correction
design
updated 2.9 years ago by
Michael Love
37k • written 3.0 years ago by
wunderl
▴ 30
0
votes
1
reply
308
views
Perform time course rna seq analysis at once with a single design or separate differential analysis for each time point
deseq2
design
updated 3.0 years ago by
Michael Love
37k • written 3.0 years ago by
adhikb
• 0
3
votes
3
replies
440
views
Extracting within subject effect in a between and within subject model with DESeq2
deseq2
design
updated 3.1 years ago by
Michael Love
37k • written 3.1 years ago by
i.sudbery
▴ 30
3
votes
5
replies
683
views
Experimental design RNAseq differential expression
edger
limma
design
contrasts
batch
updated 3.2 years ago by
Aaron Lun
★ 27k • written 3.2 years ago by
Pietro
▴ 30
3
votes
4
replies
708
views
Paired analysis (tumor vs normal) at three different conditions with EdgeR
edger
design
matrix
de
updated 3.2 years ago by
Aaron Lun
★ 27k • written 3.2 years ago by
takumima
▴ 10
0
votes
7
replies
765
views
Problems with DESeq2 'design' parameter using Shiny/rhandsontable
deseq2
shiny
design
rhandsontable
hot_to_r()
updated 3.2 years ago by
Michael Love
37k • written 3.2 years ago by
hinkel2
• 0
0
votes
1
reply
344
views
DESeq2 3 factor design - whether to split up data or add interaction terms
deseq2
design
updated 3.3 years ago by
Michael Love
37k • written 3.3 years ago by
atongz652
• 0
0
votes
2
replies
794
views
DESeq2- multifactor design- 3 conditions and 3 timepoints
deseq2
design
updated 3.3 years ago by
Michael Love
37k • written 3.3 years ago by
bioinfo
• 0
3
votes
6
replies
1.3k
views
Limma design/contrast correct?
limma
microarray
design
paired
mixed model
updated 3.3 years ago by
Aaron Lun
★ 27k • written 3.3 years ago by
rasmus.agren
• 0
4
votes
7
replies
1.5k
views
LIMMA time series spline model.matrix design setup
limma
design
model.matrix
time series
splines
updated 3.3 years ago by
Aaron Lun
★ 27k • written 3.3 years ago by
tleona3
• 0
50 results • Page
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Replies
Comment: Italicise
by
Kevin Blighe
3.5k
Okay, I am guessing that the problem is that you need to update the version of *EnhancedVolcano* to the latest version. Can you try that? T…
Comment: Italicise
by
Pau
• 0
They're the same: example of the vignette: "italic('VCAM1')" and result from my data: "italic('CARS1')" As I am running against time be…
Comment: Can Differential Isoform expression analysis can be performed using DESeq2 packa
by
priyanka.m
• 0
Thank you for the suggestions. I will try to compare my results and accordingly interpret the two.
Answer: [sva] Error in density.default(x, adjust = adj) : 'x' contains missing values
by
wahaha
• 0
I found the reason, because some gene expression levels are 0 in all samples. you can add these code to check the data: >exp_mean <- appl…
Answer: DESeq2 how to specify contrast to test difference of differences
by
Nicole
• 0
The comment from @mikelove about specifying numeric contrasts answered my question. This code is not standalone, but I will leave it here i…
Votes
Answer: DESeq2 how to specify contrast to test difference of differences
Comment: DESeq2 how to specify contrast to test difference of differences
Answer: Confused about the design matrix in edgeR: How to tell R to consider one level a
Answer: biomaRt error unable to fix: need help troubleshooting
Answer: edgeR : results from goana and kegga functions show opposite sig. p-value
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