Showing : design • reset
3
votes
6
replies
497
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 4 months ago by 48k • written 4 months ago by ▴ 10
3
votes
9
replies
896
views
Question about filter by expression (filterByExpr) in edgeR
CPM filterByExpr edgeR design model.matrix
6 months ago mohammedtoufiq91 ▴ 10
6
votes
11
replies
872
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
7 months ago mohammedtoufiq91 ▴ 10
2
votes
2
replies
400
views
Updating DESeq2 object's design with sva output
DESeq2 design sva
7 months ago Hatchet • 0
3
votes
6
replies
592
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
9 months ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
454
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
10 months ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
525
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
10 months ago mohammedtoufiq91 ▴ 10
0
votes
13
replies
1.3k
views
DESeq2 design multi factor
DESeq2 design 0substract nofullrank
updated 10 months ago by 40k • written 11 months ago by ▴ 10
0
votes
5
replies
646
views
Inquiry about suitable package for proteomics study design
Proteomics design
updated 11 months ago by • 0 • written 11 months ago by • 0
2
votes
5
replies
2.4k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 11 months ago by 40k • written 2.3 years ago by • 0
0
votes
1
reply
383
views
Design Matrix Singularity Error
DES DESIGN
updated 12 months ago by 40k • written 12 months ago by • 0
0
votes
2
replies
480
views
Design set up, interaction or group? Two Salinities treatments, Five Populations, Three Replicates
Design DESeq2
updated 16 months ago by 40k • written 16 months ago by • 0
2
votes
2
replies
967
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 16 months ago by 48k • written 16 months ago by ▴ 10
0
votes
4
replies
763
views
DESeq2 pseudotime series design?
DESeq2 design
19 months ago jordi.planells • 0
0
votes
2
replies
647
views
DeSeq2 - design formula for enrichment on combinated conditions AB, not A, not B
conditions design DESeq2 Synergy
updated 21 months ago by 40k • written 21 months ago by • 0
0
votes
1
reply
556
views
Isolate contrasts in DESeq2 while using a combination of categorical and continuous variables
Contrast design DESeq2 continuous
updated 22 months ago by 40k • written 22 months ago by • 0
1
vote
1
reply
643
views
Deseq2 contrasts and design for paired analysis
TimeSeriesExperiment RNASeq design DESeq2
updated 22 months ago by 40k • written 22 months ago by • 0
1
vote
2
replies
748
views
Which factors to include in design matrix and how to do it in a challenging experimental design
RNAseq Design Matrix
23 months ago Barista • 0
0
votes
2
replies
807
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 23 months ago by ★ 1.3k • written 23 months ago by • 0
0
votes
1
reply
454
views
Account for parent cell line when comparing isogenic mutants
interactions design DESeq2
updated 23 months ago by 40k • written 23 months ago by • 0
0
votes
2
replies
675
views
Design formula in DESeq2
model BatchEffect hidden Design DESeq2
23 months ago m.glymenaki • 0
2
votes
3
replies
1.0k
views
Contrast treated samples against both scramble and untreated controls
design contrast DESeq2
updated 23 months ago by 40k • written 23 months ago by • 0
0
votes
1
reply
1.3k
views
DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 2.1 years ago by 40k • written 2.1 years ago by • 0
0
votes
1
reply
742
views
Subject paired DESeq2 design
DESeq2 paired design
updated 2.2 years ago by 40k • written 2.2 years ago by ▴ 10
0
votes
1
reply
551
views
[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2 nesting design
updated 2.2 years ago by 40k • written 2.2 years ago by • 0
2
votes
3
replies
932
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 2.3 years ago by 48k • written 2.4 years ago by • 0
2
votes
3
replies
5.6k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 2.7 years ago by 3.8k • written 2.8 years ago by ▴ 20
0
votes
1
reply
582
views
DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2 design formula
updated 3.0 years ago by 40k • written 3.0 years ago by ▴ 20
2
votes
3
replies
645
views
EdgeR design matrix for mutlifactor RNA seq
edger design multifactor
updated 3.0 years ago by 63k • written 3.0 years ago by • 0
0
votes
5
replies
1.1k
views
DESeq2 issue with hierarchical clustering
deseq2 design
updated 3.0 years ago by 3.8k • written 3.0 years ago by • 0
2
votes
5
replies
893
views
Picking the right design formula
deseq2 design experiment
3.1 years ago donnenfieldjonah • 0
4
votes
5
replies
2.3k
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 3.1 years ago by 63k • written 3.1 years ago by • 0
2
votes
8
replies
3.4k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
3.1 years ago Pietro ▴ 40
4
votes
7
replies
798
views
Genes upregulated in one condition vs each of the other conditions
edger design
updated 3.2 years ago by 48k • written 3.2 years ago by • 0
0
votes
1
reply
581
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 3.3 years ago by 48k • written 3.3 years ago by • 0
2
votes
7
replies
1.5k
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 3.3 years ago by 48k • written 3.3 years ago by • 0
6
votes
6
replies
894
views
Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 3.6 years ago by 13k • written 3.6 years ago by • 0
0
votes
10
replies
1.8k
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 3.7 years ago by ★ 1.3k • written 3.7 years ago by • 0
1
vote
4
replies
624
views
Help with Deseq2 design
deseq2 design multifactor
updated 3.7 years ago by 40k • written 3.7 years ago by • 0
1
vote
1
reply
23k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 3.7 years ago by 40k • written 3.7 years ago by ★ 1.5k
0
votes
2
replies
701
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 3.7 years ago by 40k • written 3.7 years ago by • 0
2
votes
1
reply
901
views
combining columns for experimental design in DESeq2
deseq2 design metadata
updated 3.7 years ago by ▴ 50 • written 3.7 years ago by ★ 1.5k
1
vote
8
replies
5.6k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 2.8 years ago by 40k • written 3.9 years ago by • 0
1
vote
6
replies
1.1k
views
Relations between average expression and fold change
design AveExpr comparisons
updated 3.9 years ago by 63k • written 3.9 years ago by ▴ 720
0
votes
1
reply
1.2k
views
DESeq2 comparison of treatment within tissue type, ignoring other tissue type
deseq2 comparison design paired treatment
updated 3.9 years ago by ★ 1.3k • written 3.9 years ago by • 0
0
votes
4
replies
1.4k
views
DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2 contrast design
4.0 years ago luciest.rodriguez • 0
0
votes
2
replies
650
views
different designs for finding DEG by limma
limma DEG design
4.1 years ago amin.ghareyazi • 0
0
votes
8
replies
1.5k
views
Two controls in RNAseq formula for DESeq2
deseq2 formula controls design
updated 4.1 years ago by 40k • written 4.1 years ago by • 0
0
votes
3
replies
649
views
Analysis strategy - possible to use naive control group as t=0 for two treatment groups?
Deseq2 design time course basal group
updated 4.2 years ago by 40k • written 4.2 years ago by • 0
4
votes
18
replies
22k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 4.3 years ago by • 0 • written 8.9 years ago by ▴ 100
50 results • Page 1 of 1
Recent ...
Replies
Comment: Exporting DESeq2 filtered results by James W. MacDonald 63k
I am interested to know what part of my response you found rude. I asked nicely that you don't add to ancient posts, said your post isn't r…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
> I can imagine writing a sparse high-dimensional array in HDF5, but I'm still not sure how to implement the part where it is read and imme…
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Not in BioC 3.18. At some point (e.g. in 6 months) they will be deprecated, then 6 months later (i.e. in 1 year) they will be defunct, then…
Comment: Biostrings error at retrieving protein sequences by Hervé Pagès 16k
Yes, but you need to put the clean names back on the AAStringSet object: ``` names(protein_sequences) <- gsub(" .*", "", names(protein_sequ…
Comment: Exporting DESeq2 filtered results by camillab. ▴ 10
thanks! I didn't`t notice that. I will cancel it now!
Votes
Batch Effect in DESeq2, how to control, how to remove it, how to address biological question
A: BiomaRt Arabidopsis genome unavailable
Answer: enrichKEGG
A: Effect of lfcThreshold on p-value in DESeq2
Comment: Mixed up sample info with plotPCA
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