Showing : Design • reset
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DESeq2 time course and dosage response
LRT Design DESeq2 doseResponse TimeSeriesExperiment
updated 4 weeks ago by 34k • written 4 weeks ago by • 0
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1
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85
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Subject paired DESeq2 design
DESeq2 paired design
updated 6 weeks ago by 34k • written 6 weeks ago by ▴ 10
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1
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152
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[DESeq2] Question regarding experiment design with multiple nesting and variables
DESeq2 nesting design
updated 7 weeks ago by 34k • written 10 weeks ago by • 0
2
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3
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243
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DESeq2 with two continuous variable in a design
DESeq2 RNASeq R design
updated 9 weeks ago by 34k • written 11 weeks ago by • 0
2
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3
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202
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Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 3 months ago by 43k • written 3 months ago by • 0
2
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3
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384
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DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 8 months ago by 3.4k • written 8 months ago by ▴ 10
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1
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140
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DeSeq2 4 different formulas but 4 times the same heatmap...
deseq2 design formula
updated 11 months ago by 34k • written 11 months ago by ▴ 20
2
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3
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228
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EdgeR design matrix for mutlifactor RNA seq
edger design multifactor
updated 11 months ago by 58k • written 11 months ago by • 0
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5
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269
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DESeq2 issue with hierarchical clustering
deseq2 design
updated 12 months ago by 3.4k • written 12 months ago by • 0
2
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5
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301
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Picking the right design formula
deseq2 design experiment
12 months ago donnenfieldjonah • 0
2
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5
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550
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How to incorporate batch effect that is only present in one level into the design?
linear model batch effect DESeq2 design
updated 13 months ago by 58k • written 13 months ago by • 0
2
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8
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857
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Remove batch effect limma, "Coefficients not estimable" warning and design matrix
limma deseq2 batch design batch effect
13 months ago Pietro ▴ 30
4
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7
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260
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Genes upregulated in one condition vs each of the other conditions
edger design
updated 14 months ago by 43k • written 14 months ago by • 0
0
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181
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Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 15 months ago by 43k • written 15 months ago by • 0
2
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7
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344
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Limma analysis with multiple variables
limma model.matrix de design rnaseq
updated 15 months ago by 43k • written 15 months ago by • 0
6
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6
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302
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Design to analyze experiment with multiple samples from the same biological entity
rna-seq design linear model glm
updated 19 months ago by 13k • written 19 months ago by • 0
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10
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375
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DEseq2 design formula correcting for batch
deseq2 design formula batch effect
updated 19 months ago by ▴ 850 • written 19 months ago by • 0
1
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4
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214
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Help with Deseq2 design
deseq2 design multifactor
updated 20 months ago by 34k • written 20 months ago by • 0
1
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1
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4.5k
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lfcShrink doesn't work with contrasts
lfcShrink contrast design deseq2
updated 20 months ago by 34k • written 20 months ago by ★ 1.5k
0
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2
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178
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Design of time-course experiment in DESeq2
deseq2 design design formula time course lrt
updated 20 months ago by 34k • written 20 months ago by • 0
2
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1
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168
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combining columns for experimental design in DESeq2
deseq2 design metadata
updated 20 months ago by ▴ 50 • written 20 months ago by ★ 1.5k
1
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8
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1.7k
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DESeq2: Continuous and discreate variables in the design
deseq2 R rna-seq design
updated 8 months ago by 34k • written 22 months ago by • 0
1
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6
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264
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Relations between average expression and fold change
design AveExpr comparisons
updated 22 months ago by 58k • written 22 months ago by ▴ 650
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379
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DESeq2 comparison of treatment within tissue type, ignoring other tissue type
deseq2 comparison design paired treatment
updated 22 months ago by ▴ 850 • written 22 months ago by • 0
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4
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691
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DESeq2: compare all tpts to baseline and pull results table accordingly
deseq2 contrast design
23 months ago luciest.rodriguez • 0
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2
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279
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different designs for finding DEG by limma
limma DEG design
2.0 years ago amin.ghareyazi • 0
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8
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508
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Two controls in RNAseq formula for DESeq2
deseq2 formula controls design
updated 2.1 years ago by 34k • written 2.1 years ago by • 0
0
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3
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244
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Analysis strategy - possible to use naive control group as t=0 for two treatment groups?
Deseq2 design time course basal group
updated 2.2 years ago by 34k • written 2.2 years ago by • 0
2
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18
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17k
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DEseq2 time-series design.
deseq2 timecourse design
updated 2.2 years ago by • 0 • written 6.9 years ago by ▴ 90
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1
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250
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DESeq2 analysis of multifactorial RNAseq experiment
deseq2 design time-course
updated 2.2 years ago by 34k • written 2.2 years ago by • 0
1
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1
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299
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All Pairwise Comparisons with DESeq2 While Controlling for Batch Effects: Does Reference Level Matter?
deseq2 differential expression batch correction design
updated 2.3 years ago by 34k • written 2.3 years ago by ▴ 30
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234
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Perform time course rna seq analysis at once with a single design or separate differential analysis for each time point
deseq2 design
updated 2.3 years ago by 34k • written 2.3 years ago by • 0
3
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3
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332
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Extracting within subject effect in a between and within subject model with DESeq2
deseq2 design
updated 2.4 years ago by 34k • written 2.4 years ago by ▴ 20
3
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5
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523
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Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 2.5 years ago by ★ 27k • written 2.5 years ago by ▴ 30
3
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4
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436
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Paired analysis (tumor vs normal) at three different conditions with EdgeR
edger design matrix de
updated 2.5 years ago by ★ 27k • written 2.5 years ago by ▴ 10
0
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7
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616
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Problems with DESeq2 'design' parameter using Shiny/rhandsontable
deseq2 shiny design rhandsontable hot_to_r()
updated 2.5 years ago by 34k • written 2.5 years ago by • 0
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254
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DESeq2 3 factor design - whether to split up data or add interaction terms
deseq2 design
updated 2.6 years ago by 34k • written 2.6 years ago by • 0
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2
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509
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DESeq2- multifactor design- 3 conditions and 3 timepoints
deseq2 design
updated 2.6 years ago by 34k • written 2.6 years ago by • 0
3
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6
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756
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Limma design/contrast correct?
limma microarray design paired mixed model
updated 2.6 years ago by ★ 27k • written 2.6 years ago by • 0
4
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7
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1.2k
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LIMMA time series spline model.matrix design setup
limma design model.matrix time series splines
updated 2.6 years ago by ★ 27k • written 2.6 years ago by • 0
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2
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387
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DESeq2 design with different cell lines and disease status
deseq2 design
updated 2.6 years ago by 34k • written 2.6 years ago by • 0
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7
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674
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DeSeq2 Ribosome Profiling: multiple factor design
deseq2 design timeseries
updated 2.7 years ago by 34k • written 2.7 years ago by ▴ 20
7
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7
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6.3k
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DESeq2 likelihood ratio test (LRT) design - 2 genotypes, 4 time points
deseq2 LRT rnaseq design reduced model
updated 2.8 years ago by • 0 • written 4.4 years ago by ▴ 50
5
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6
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715
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How to set up appropriate analysis using sample type and condition for DESeq2
deseq2 differential gene expression design
updated 2.9 years ago by 34k • written 2.9 years ago by • 0
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5
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616
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DESeq2 design formula - correlation with ordered variable
DESeq2 design formula matrix
updated 3.3 years ago by 34k • written 3.3 years ago by 170
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4
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496
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Limma model for paired and pool together
limma design rnaseq
updated 3.4 years ago by 7.6k • written 3.4 years ago by ▴ 340
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5
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535
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DESeq2 It is correct to use interaction term for patient variability?
deseq2 design interaction term R
3.6 years ago • updated 3.5 years ago briverog • 0
1
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8
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653
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design versus interaction term similarities and/or differences?
deseq2 ANOVA design interaction term
updated 3.6 years ago by 34k • written 3.6 years ago by • 0
1
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2
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875
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DESeq2 - Design for TCGA unpaired RNAseq data
DESeq2 design TCGA unpaired RNAseq
updated 3.7 years ago by 34k • written 3.7 years ago by ▴ 10
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5
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687
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Limma: how to account for twin data (both MZ and DZ twins)?
limma design RNA-seq formula twins
updated 3.9 years ago by ★ 27k • written 3.9 years ago by • 0
50 results • Page 1 of 1
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Answer: Undefined columns error R cytometry analysis by Jiang, Mike ★ 1.3k
I see you are trying to fill the missing transform info to `gs_bcell_auto` , which is a hack, but since you seems to know what you are doin…
Comment: how to get MFI stats from data by Jiang, Mike ★ 1.3k
Can you grant the public caccess to you fcs to reproduce your issue?
Answer: Getting a dataset that only contains the flow data within the gated area by Jiang, Mike ★ 1.3k
You didn't post your example code, so here is my best guess of your workflow > library(flowCore) > library(flowWorkspace) …
Comment: Diffbind dba.plotProfile attempt to select less than one element in OneIndex by bhanratt • 0
``` > DBA 10 Samples, 31953 sites in matrix: ID Tissue Factor Condition Replicate Reads FRiP 1 58 1 H3K4me3 AD …
Answer: Warning messages on Apple M1 BigSur by Vincent J. Carey, Jr. 6.5k
We are not producing M1 binaries at this time. If you use the intel version of R under Rosetta 2 you can use the intel mac binaries.
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Comment: Use of coef() as a measure of effect size in a multiple regression using DESeq2
Answer: Log fold change interpretation of time series with Wald test
A: gviz: name of tracks disappeas
Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
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Scholar to Jiang, Mike ★ 1.3k
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