Showing : Design • reset
6
votes
6
replies
2.8k
views
design matrix for 4 groups in edgeR
edger design
9.5 years ago alakatos ▴ 130
2
votes
8
replies
2.4k
views
DESeq design question
deseq2 design
9.4 years ago • updated 9.1 years ago sunkid • 0
4
votes
18
replies
24k
views
DEseq2 time-series design.
deseq2 timecourse design
updated 4.8 years ago by • 0 • written 9.5 years ago by ▴ 100
4
votes
13
replies
2.5k
views
Which formula should I use to set the best model matrix for my analysis ?
DESEQ2 EDGER design
7.5 years ago ZheFrench ▴ 40
3
votes
13
replies
2.2k
views
Design and independent filtering of patient RNA-seq data
differential gene expression deseq2 design independent filtering limma
updated 8.9 years ago by 65k • written 8.9 years ago by ▴ 90
6
votes
11
replies
1.4k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
14 months ago mohammedtoufiq91 ▴ 10
0
votes
3
replies
815
views
Analysis strategy - possible to use naive control group as t=0 for two treatment groups?
Deseq2 design time course basal group
updated 4.8 years ago by 41k • written 4.8 years ago by • 0
0
votes
8
replies
1.9k
views
Two controls in RNAseq formula for DESeq2
deseq2 formula controls design
updated 4.7 years ago by 41k • written 4.7 years ago by • 0
0
votes
2
replies
996
views
DESeq2 interaction terms in 2x2x2 factorial design
Interactions design Multifactorial DESeq2
updated 2.5 years ago by ★ 1.3k • written 2.5 years ago by • 0
2
votes
5
replies
3.2k
views
DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 18 months ago by 41k • written 2.8 years ago by • 0
0
votes
13
replies
2.1k
views
DESeq2 design multi factor
DESeq2 design 0substract nofullrank
updated 17 months ago by 41k • written 18 months ago by ▴ 10
0
votes
4
replies
1.7k
views
DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2 contrast design
4.5 years ago luciest.rodriguez • 0
4
votes
7
replies
1.1k
views
Genes upregulated in one condition vs each of the other conditions
edger design
updated 3.8 years ago by 50k • written 3.8 years ago by • 0
4
votes
5
replies
2.9k
views
How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 3.7 years ago by 65k • written 3.7 years ago by • 0
0
votes
5
replies
981
views
Inquiry about suitable package for proteomics study design
Proteomics design
updated 18 months ago by • 0 • written 18 months ago by • 0
1
vote
8
replies
1.5k
views
design versus interaction term similarities and/or differences?
deseq2 ANOVA design interaction term
updated 6.2 years ago by 41k • written 6.2 years ago by • 0
0
votes
5
replies
1.4k
views
DESeq2 It is correct to use interaction term for patient variability?
deseq2 design interaction term R
6.2 years ago • updated 6.1 years ago briverog • 0
2
votes
4
replies
914
views
Limma model for paired and pool together
limma design rnaseq
updated 6.0 years ago by ★ 7.9k • written 6.0 years ago by ▴ 360
0
votes
5
replies
1.3k
views
DESeq2 design formula - correlation with ordered variable
DESeq2 design formula matrix
updated 5.9 years ago by 41k • written 5.9 years ago by ▴ 170
5
votes
6
replies
1.5k
views
How to set up appropriate analysis using sample type and condition for DESeq2
deseq2 differential gene expression design
updated 5.5 years ago by 41k • written 5.5 years ago by • 0
0
votes
7
replies
1.3k
views
DeSeq2 Ribosome Profiling: multiple factor design
deseq2 design timeseries
updated 5.3 years ago by 41k • written 5.3 years ago by ▴ 20
3
votes
6
replies
2.6k
views
Limma design/contrast correct?
limma microarray design paired mixed model
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
0
votes
2
replies
1.6k
views
DESeq2- multifactor design- 3 conditions and 3 timepoints
deseq2 design
updated 5.2 years ago by 41k • written 5.2 years ago by • 0
0
votes
1
reply
585
views
DESeq2 3 factor design - whether to split up data or add interaction terms
deseq2 design
updated 5.2 years ago by 41k • written 5.2 years ago by • 0
0
votes
7
replies
1.5k
views
Problems with DESeq2 'design' parameter using Shiny/rhandsontable
deseq2 shiny design rhandsontable hot_to_r()
updated 5.1 years ago by 41k • written 5.1 years ago by • 0
3
votes
4
replies
1.3k
views
Paired analysis (tumor vs normal) at three different conditions with EdgeR
edger design matrix de
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 10
3
votes
5
replies
1.4k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 40
3
votes
3
replies
781
views
Extracting within subject effect in a between and within subject model with DESeq2
deseq2 design
updated 5.0 years ago by 41k • written 5.0 years ago by ▴ 40
0
votes
1
reply
618
views
Perform time course rna seq analysis at once with a single design or separate differential analysis for each time point
deseq2 design
updated 4.9 years ago by 41k • written 4.9 years ago by • 0
1
vote
1
reply
991
views
All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2 differential expression batch correction design
updated 4.9 years ago by 41k • written 4.9 years ago by ▴ 40
0
votes
1
reply
634
views
DESeq2 analysis of multifactorial RNAseq experiment
deseq2 design time-course
updated 4.8 years ago by 41k • written 4.8 years ago by • 0
0
votes
1
reply
1.4k
views
DESeq2 comparison of treatment within tissue type, ignoring other tissue type
deseq2 comparison design paired treatment
updated 4.4 years ago by ★ 1.3k • written 4.4 years ago by • 0
1
vote
6
replies
1.4k
views
Relations between average expression and fold change
design AveExpr comparisons
updated 4.4 years ago by 65k • written 4.4 years ago by ▴ 730
1
vote
8
replies
7.1k
views
DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 3.3 years ago by 41k • written 4.4 years ago by • 0
2
votes
1
reply
1.2k
views
combining columns for experimental design in DESeq2
deseq2 design metadata
updated 4.3 years ago by ▴ 50 • written 4.3 years ago by ★ 1.5k
0
votes
2
replies
951
views
Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 4.3 years ago by 41k • written 4.3 years ago by • 0
1
vote
1
reply
25k
views
lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 4.3 years ago by 41k • written 4.3 years ago by ★ 1.5k
1
vote
4
replies
806
views
Help with Deseq2 design
deseq2 design multifactor
updated 4.3 years ago by 41k • written 4.3 years ago by • 0
0
votes
10
replies
2.4k
views
DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 4.2 years ago by ★ 1.3k • written 4.2 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 4.2 years ago by ★ 13k • written 4.2 years ago by • 0
2
votes
7
replies
2.0k
views
Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 3.9 years ago by 50k • written 3.9 years ago by • 0
0
votes
1
reply
792
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 3.9 years ago by 50k • written 3.9 years ago by • 0
2
votes
8
replies
4.2k
views
Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
3.7 years ago Pietro ▴ 40
2
votes
5
replies
1.1k
views
Picking the right design formula
deseq2 design experiment
3.6 years ago donnenfieldjonah • 0
0
votes
5
replies
1.6k
views
DESeq2 issue with hierarchical clustering
deseq2 design
updated 3.6 years ago by ★ 3.9k • written 3.6 years ago by • 0
2
votes
3
replies
825
views
EdgeR design matrix for mutlifactor RNA seq
edger design multifactor
updated 3.5 years ago by 65k • written 3.5 years ago by • 0
0
votes
1
reply
747
views
DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2 design formula
updated 3.5 years ago by 41k • written 3.5 years ago by ▴ 40
0
votes
2
replies
922
views
Design formula in DESeq2
model BatchEffect hidden Design DESeq2
2.5 years ago m.glymenaki • 0
2
votes
3
replies
7.4k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 3.3 years ago by ★ 3.9k • written 3.3 years ago by ▴ 30
0
votes
2
replies
669
views
Design set up, interaction or group? Two Salinities treatments, Five Populations, Three Replicates
Design DESeq2
updated 22 months ago by 41k • written 22 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough?
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
I am not sure how your comment helps here?
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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