Showing : design • reset
2
votes
3
replies
255
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 4 weeks ago by 51k • written 4 weeks ago by • 0
0
votes
6
replies
369
views
Once again a "Model matrix not full rank"
DESeq2 design coldata
updated 6 weeks ago by ★ 1.4k • written 6 weeks ago by ▴ 130
2
votes
3
replies
342
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 12 weeks ago by 51k • written 3 months ago by • 0
2
votes
2
replies
324
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
3 months ago Sabiha ▴ 20
2
votes
2
replies
331
views
Limma design for 3 replicated time courses comparing treatment vs placebo
design limma
4 months ago SamGG ▴ 350
3
votes
6
replies
906
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 12 months ago by 51k • written 12 months ago by ▴ 10
3
votes
9
replies
1.9k
views
Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
14 months ago mohammedtoufiq91 ▴ 10
6
votes
11
replies
1.4k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
16 months ago mohammedtoufiq91 ▴ 10
2
votes
2
replies
915
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
16 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
18 months ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
831
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
18 months ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
817
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
18 months ago mohammedtoufiq91 ▴ 10
0
votes
13
replies
2.2k
views
DESeq2 design multi factor
DESeq2 design 0substract nofullrank
updated 19 months ago by 42k • written 20 months ago by ▴ 10
0
votes
5
replies
1.1k
views
Inquiry about suitable package for proteomics study design
Proteomics design
updated 20 months ago by • 0 • written 20 months ago by • 0
2
votes
5
replies
3.4k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 20 months ago by 42k • written 3.0 years ago by • 0
0
votes
1
reply
594
views
Design Matrix Singularity Error
DES DESIGN
updated 21 months ago by 42k • written 21 months ago by • 0
0
votes
2
replies
730
views
Design set up, interaction or group? Two Salinities treatments, Five Populations, Three Replicates
Design DESeq2
updated 2.0 years ago by 42k • written 2.0 years ago by • 0
2
votes
2
replies
1.6k
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 2.1 years ago by 51k • written 2.1 years ago by ▴ 10
0
votes
4
replies
1.1k
views
DESeq2 pseudotime series design?
DESeq2 design
2.3 years ago jordi.planells • 0
0
votes
2
replies
893
views
DeSeq2 - design formula for enrichment on combinated conditions AB, not A, not B
conditions design DESeq2 Synergy
updated 2.5 years ago by 42k • written 2.5 years ago by • 0
0
votes
1
reply
776
views
Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 2.5 years ago by 42k • written 2.5 years ago by • 0
1
vote
1
reply
818
views
Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 2.5 years ago by 42k • written 2.5 years ago by • 0
1
vote
2
replies
1.0k
views
Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq Design Matrix
2.6 years ago Barista • 0
0
votes
2
replies
1.1k
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 2.6 years ago by ★ 1.4k • written 2.6 years ago by • 0
0
votes
1
reply
643
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 2.6 years ago by 42k • written 2.6 years ago by • 0
0
votes
2
replies
998
views
Design formula in DESeq2
model BatchEffect hidden Design DESeq2
2.6 years ago m.glymenaki • 0
2
votes
3
replies
1.3k
views
Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 2.7 years ago by 42k • written 2.7 years ago by • 0
0
votes
1
reply
1.8k
views
DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 2.8 years ago by 42k • written 2.8 years ago by • 0
0
votes
1
reply
973
views
Subject paired DESeq2 design
DESeq2 paired design
updated 2.9 years ago by 42k • written 2.9 years ago by ▴ 10
0
votes
1
reply
716
views
[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2 nesting design
updated 2.9 years ago by 42k • written 2.9 years ago by • 0
2
votes
3
replies
1.2k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 3.0 years ago by 51k • written 3.1 years ago by • 0
2
votes
3
replies
7.8k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 3.4 years ago by ★ 3.9k • written 3.5 years ago by ▴ 30
0
votes
1
reply
777
views
DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2 design formula
updated 3.7 years ago by 42k • written 3.7 years ago by ▴ 50
2
votes
3
replies
869
views
EdgeR design matrix for mutlifactor RNA seq
edger design multifactor
updated 3.7 years ago by 66k • written 3.7 years ago by • 0
0
votes
5
replies
1.7k
views
DESeq2 issue with hierarchical clustering
deseq2 design
updated 3.7 years ago by ★ 3.9k • written 3.7 years ago by • 0
2
votes
5
replies
1.2k
views
Picking the right design formula
deseq2 design experiment
3.8 years ago donnenfieldjonah • 0
4
votes
5
replies
3.0k
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 3.8 years ago by 66k • written 3.8 years ago by • 0
2
votes
8
replies
4.4k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
3.8 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 3.9 years ago by 51k • written 3.9 years ago by • 0
0
votes
1
reply
829
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 4.0 years ago by 51k • written 4.0 years ago by • 0
2
votes
7
replies
2.1k
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 4.0 years ago by 51k • written 4.0 years ago by • 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 4.3 years ago by ★ 13k • written 4.3 years ago by • 0
0
votes
10
replies
2.5k
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 4.4 years ago by ★ 1.4k • written 4.4 years ago by • 0
1
vote
4
replies
853
views
Help with Deseq2 design
deseq2 design multifactor
updated 4.4 years ago by 42k • written 4.4 years ago by • 0
1
vote
1
reply
25k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 4.4 years ago by 42k • written 4.4 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 4.4 years ago by 42k • written 4.4 years ago by • 0
2
votes
1
reply
1.3k
views
combining columns for experimental design in DESeq2
deseq2 design metadata
updated 4.4 years ago by ▴ 50 • written 4.4 years ago by ★ 1.5k
1
vote
8
replies
7.5k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 3.5 years ago by 42k • written 4.6 years ago by • 0
1
vote
6
replies
1.5k
views
Relations between average expression and fold change
design AveExpr comparisons
updated 4.6 years ago by 66k • written 4.6 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 4.6 years ago by ★ 1.4k • written 4.6 years ago by • 0
50 results • Page 1 of 1
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Comment: Trouble reading samplesheet in with diffbind to create dba by Mallory • 0
Thank you for your reply! There mustve been something wierd going on with my peak formats as you pointed out. I recalled all the peaks and …
Answer: Trouble reading samplesheet in with diffbind to create dba by Anthony • 0
I was struggling with this today too. For me it happened because my peak files were not in the correct format. The "10 elements" refers to …
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Votes
Answer: How to do DESeq2 on Kallisto Data
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
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