Showing : DESIGN • reset
3
votes
3
replies
373
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 10 weeks ago by 51k • written 10 weeks ago by • 0
0
votes
6
replies
454
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 11 weeks ago by ★ 1.4k • written 12 weeks ago by ▴ 130
2
votes
3
replies
404
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 4 months ago by 51k • written 4 months ago by • 0
2
votes
2
replies
369
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
4 months ago Sabiha ▴ 20
2
votes
2
replies
368
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
5 months ago SamGG ▴ 350
3
votes
6
replies
962
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 14 months ago by 51k • written 14 months ago by ▴ 10
3
votes
9
replies
2.0k
views
Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
16 months ago mohammedtoufiq91 ▴ 10
6
votes
11
replies
1.5k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
17 months ago mohammedtoufiq91 ▴ 10
2
votes
2
replies
954
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
17 months ago Hatchet • 0
3
votes
6
replies
1.1k
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
19 months ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
867
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
19 months ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
852
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
20 months ago mohammedtoufiq91 ▴ 10
0
votes
13
replies
2.4k
views
DESeq2 design multi factor
DESeq2 design 0substract nofullrank
updated 20 months ago by 42k • written 21 months ago by ▴ 10
0
votes
5
replies
1.1k
views
Inquiry about suitable package for proteomics study design
Proteomics design
updated 21 months ago by • 0 • written 21 months ago by • 0
2
votes
5
replies
3.6k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 21 months ago by 42k • written 3.1 years ago by • 0
0
votes
1
reply
627
views
Design Matrix Singularity Error
DES DESIGN
updated 22 months ago by 42k • written 22 months ago by • 0
0
votes
2
replies
771
views
Design set up, interaction or group? Two Salinities treatments, Five Populations, Three Replicates
Design DESeq2
updated 2.1 years ago by 42k • written 2.1 years ago by • 0
2
votes
2
replies
1.7k
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 2.2 years ago by 51k • written 2.2 years ago by ▴ 10
0
votes
4
replies
1.1k
views
DESeq2 pseudotime series design?
DESeq2 design
2.4 years ago jordi.planells • 0
0
votes
2
replies
924
views
DeSeq2 - design formula for enrichment on combinated conditions AB, not A, not B
conditions design DESeq2 Synergy
updated 2.6 years ago by 42k • written 2.6 years ago by • 0
0
votes
1
reply
804
views
Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 2.6 years ago by 42k • written 2.6 years ago by • 0
1
vote
1
reply
848
views
Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 2.6 years ago by 42k • written 2.6 years ago by • 0
1
vote
2
replies
1.1k
views
Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq Design Matrix
2.7 years ago Barista • 0
0
votes
2
replies
1.1k
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 2.7 years ago by ★ 1.4k • written 2.7 years ago by • 0
0
votes
1
reply
673
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 2.7 years ago by 42k • written 2.7 years ago by • 0
0
votes
2
replies
1.1k
views
Design formula in DESeq2
model BatchEffect hidden Design DESeq2
2.7 years ago m.glymenaki • 0
2
votes
3
replies
1.4k
views
Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 2.8 years ago by 42k • written 2.8 years ago by • 0
0
votes
1
reply
1.8k
views
DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 2.9 years ago by 42k • written 2.9 years ago by • 0
0
votes
1
reply
1.0k
views
Subject paired DESeq2 design
DESeq2 paired design
updated 3.0 years ago by 42k • written 3.0 years ago by ▴ 10
0
votes
1
reply
742
views
[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2 nesting design
updated 3.0 years ago by 42k • written 3.1 years ago by • 0
2
votes
3
replies
1.3k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 3.2 years ago by 51k • written 3.2 years ago by • 0
2
votes
3
replies
8.2k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 3.6 years ago by ★ 4.0k • written 3.6 years ago by ▴ 30
0
votes
1
reply
799
views
DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2 design formula
updated 3.8 years ago by 42k • written 3.8 years ago by ▴ 50
2
votes
3
replies
903
views
EdgeR design matrix for mutlifactor RNA seq
edger design multifactor
updated 3.8 years ago by 66k • written 3.8 years ago by • 0
0
votes
5
replies
1.8k
views
DESeq2 issue with hierarchical clustering
deseq2 design
updated 3.9 years ago by ★ 4.0k • written 3.9 years ago by • 0
2
votes
5
replies
1.2k
views
Picking the right design formula
deseq2 design experiment
3.9 years ago donnenfieldjonah • 0
4
votes
5
replies
3.1k
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 3.9 years ago by 66k • written 3.9 years ago by • 0
2
votes
8
replies
4.6k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
3.9 years ago Pietro ▴ 40
4
votes
7
replies
1.2k
views
Genes upregulated in one condition vs each of the other conditions
edger design
updated 4.0 years ago by 51k • written 4.0 years ago by • 0
0
votes
1
reply
859
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 4.1 years ago by 51k • written 4.1 years ago by • 0
2
votes
7
replies
2.2k
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 4.1 years ago by 51k • written 4.1 years ago by • 0
6
votes
6
replies
1.3k
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 4.5 years ago by ★ 13k • written 4.5 years ago by • 0
0
votes
10
replies
2.7k
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 4.5 years ago by ★ 1.4k • written 4.5 years ago by • 0
1
vote
4
replies
911
views
Help with Deseq2 design
deseq2 design multifactor
updated 4.5 years ago by 42k • written 4.5 years ago by • 0
1
vote
1
reply
26k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 4.5 years ago by 42k • written 4.5 years ago by ★ 1.5k
0
votes
2
replies
1.1k
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 4.5 years ago by 42k • written 4.5 years ago by • 0
2
votes
1
reply
1.4k
views
combining columns for experimental design in DESeq2
deseq2 design metadata
updated 4.6 years ago by ▴ 50 • written 4.6 years ago by ★ 1.5k
1
vote
8
replies
7.8k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 3.6 years ago by 42k • written 4.7 years ago by • 0
1
vote
6
replies
1.6k
views
Relations between average expression and fold change
design AveExpr comparisons
updated 4.7 years ago by 66k • written 4.7 years ago by ▴ 730
0
votes
1
reply
1.5k
views
DESeq2 comparison of treatment within tissue type, ignoring other tissue type
deseq2 comparison design paired treatment
updated 4.7 years ago by ★ 1.4k • written 4.7 years ago by • 0
50 results • Page 1 of 1
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Comment: 'path' must be string by James W. MacDonald 66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string by cpierce2 • 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest by Robert • 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta by Guido Hooiveld ★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta by Michael Love 42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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Scholar to Michael Love 42k
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Scholar to Gordon Smyth 51k
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