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 45k • written 14 days ago by ▴ 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 37k • written 5 months ago by • 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 37k • written 5 months ago by • 0
1
vote
1
reply
238
views
Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 5 months ago by 37k • written 5 months ago by • 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 ★ 1.0k • written 6 months ago by • 0
0
votes
1
reply
167
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 6 months ago by 37k • written 6 months ago by • 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 37k • written 7 months ago by • 0
0
votes
1
reply
419
views
DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 9 months ago by 37k • written 9 months ago by • 0
0
votes
1
reply
210
views
Subject paired DESeq2 design
DESeq2 paired design
updated 9 months ago by 37k • written 9 months ago by ▴ 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 37k • written 10 months ago by • 0
2
votes
3
replies
748
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 10 months ago by 37k • written 11 months ago by • 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 45k • written 12 months ago by • 0
2
votes
3
replies
1.5k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 16 months ago by 3.5k • written 17 months ago by ▴ 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 37k • written 19 months ago by ▴ 20
2
votes
3
replies
351
views
EdgeR design matrix for mutlifactor RNA seq
edger design multifactor
updated 19 months ago by 60k • written 19 months ago by • 0
0
votes
5
replies
427
views
DESeq2 issue with hierarchical clustering
deseq2 design
updated 20 months ago by 3.5k • written 20 months ago by • 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 60k • written 21 months ago by • 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 45k • written 22 months ago by • 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 45k • written 23 months ago by • 0
2
votes
7
replies
624
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 23 months ago by 45k • written 23 months ago by • 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 13k • written 2.3 years ago by • 0
0
votes
10
replies
634
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 2.3 years ago by ★ 1.0k • written 2.3 years ago by • 0
1
vote
4
replies
319
views
Help with Deseq2 design
deseq2 design multifactor
updated 2.3 years ago by 37k • written 2.3 years ago by • 0
1
vote
1
reply
13k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 2.4 years ago by 37k • written 2.4 years ago by ★ 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 37k • written 2.4 years ago by • 0
2
votes
1
reply
264
views
combining columns for experimental design in DESeq2
deseq2 design metadata
updated 2.4 years ago by ▴ 50 • written 2.4 years ago by ★ 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 37k • written 2.5 years ago by • 0
1
vote
6
replies
522
views
Relations between average expression and fold change
design AveExpr comparisons
updated 2.5 years ago by 60k • written 2.5 years ago by ▴ 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 ★ 1.0k • written 2.5 years ago by • 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 37k • written 2.8 years ago by • 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 37k • written 2.9 years ago by • 0
2
votes
18
replies
18k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 2.9 years ago by • 0 • written 7.6 years ago by ▴ 90
0
votes
1
reply
324
views
DESeq2 analysis of multifactorial RNAseq experiment
deseq2 design time-course
updated 2.9 years ago by 37k • written 2.9 years ago by • 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 37k • written 3.0 years ago by ▴ 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 37k • written 3.0 years ago by • 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 37k • written 3.1 years ago by ▴ 30
3
votes
5
replies
683
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 3.2 years ago by ★ 27k • written 3.2 years ago by ▴ 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 ★ 27k • written 3.2 years ago by ▴ 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 37k • written 3.2 years ago by • 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 37k • written 3.3 years ago by • 0
0
votes
2
replies
794
views
DESeq2- multifactor design- 3 conditions and 3 timepoints
deseq2 design
updated 3.3 years ago by 37k • written 3.3 years ago by • 0
3
votes
6
replies
1.3k
views
Limma design/contrast correct?
limma microarray design paired mixed model
updated 3.3 years ago by ★ 27k • written 3.3 years ago by • 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 ★ 27k • written 3.3 years ago by • 0
50 results • Page 1 of 1
Recent ...
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
Awards • All
Scholar to Nicole • 0
Teacher to Michael Love 37k
Popular Question to svlachavas ▴ 780
Popular Question to Gordon Smyth 45k
Scholar to Rory Stark ★ 4.4k
Locations • All
United Kingdom, 23 minutes ago
France, 26 minutes ago
WEHI, Melbourne, Australia, 49 minutes ago
Seattle, 1 hour ago
China, 1 hour ago
Traffic: 194 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6