Showing : DifferentialExpression • reset
12
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13
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13k
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GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 23 months ago by ★ 5.0k • written 3.8 years ago by ▴ 70
8
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5
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3.6k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 14 months ago by 53k • written 22 months ago by ▴ 60
6
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2
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4.4k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by ▴ 10
6
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3
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2.0k
views
differential gene expression
limma differentialexpression
updated 11.3 years ago by ▴ 760 • written 11.3 years ago by ▴ 20
6
votes
11
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2.5k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
2.9 years ago mohammedtoufiq91 ▴ 10
5
votes
4
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12k
views
DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 3.8 years ago by • 0 • written 4.4 years ago by ▴ 10
5
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2
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3.7k
views
Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 3.4 years ago by 53k • written 4.4 years ago by ▴ 10
5
votes
6
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1.6k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 21 months ago by ★ 5.0k • written 21 months ago by ▴ 70
5
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6
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1.6k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
24 months ago Shaimaa Gamal • 0
5
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6
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2.8k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 4.9 years ago by ★ 29k • written 4.9 years ago by • 0
5
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9
replies
2.4k
views
Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 4.5 years ago by 68k • written 4.5 years ago by ▴ 840
4
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5
replies
2.5k
views
What to do if covariates in design matrix of limma are confounded
limma DifferentialExpression
updated 3.7 years ago by • 0 • written 3.9 years ago by ▴ 70
4
votes
2
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7.5k
views
DESeq2: removing levels from a factor or not having them in the analysis at all
deseq2 differentialexpression
updated 11.3 years ago by 43k • written 11.3 years ago by ▴ 110
4
votes
3
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1.8k
views
Limma/voom analysis of time-series data (with only 1 condition)
limma DifferentialExpression
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
4
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6
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1.7k
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 23 months ago by 53k • written 2.0 years ago by • 0
4
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10
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2.2k
views
Paired Time course Experiment Design on edgeR between and within groups
edgeR diffcyt limma DifferentialExpression
5.2 years ago Hajar • 0
4
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3
replies
1.2k
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 23 months ago by 53k • written 23 months ago by • 0
3
votes
6
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3.0k
views
Repeated measures per individual and unbalanced number of measures per individual: DE between groups still an ordinary two-group comparison?
differentialexpression deseq2 limma edger repeatedmeasures
6.3 years ago • updated 4.0 years ago hermidalc ▴ 20
3
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4
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2.1k
views
How to make design matrices or compare contrast in limma
designmatrices differentialexpression makeContrasts limma model.matrix
3.8 years ago mohammedtoufiq91 ▴ 10
3
votes
2
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1.1k
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
23 months ago Shaimaa Gamal • 0
3
votes
3
replies
999
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 14 months ago by 53k • written 14 months ago by • 0
3
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7
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2.0k
views
Getting differentially expressed genes for time points
edgeR DifferentialExpression limma
updated 4.9 years ago by 53k • written 4.9 years ago by ▴ 20
3
votes
3
replies
1.8k
views
the count matrix have decimal values
DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by • 0
3
votes
6
replies
2.4k
views
do I have to do this step in creating DGEList ?
DifferentialExpression
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
3
votes
3
replies
2.0k
views
Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
DifferentialExpression DESeq2
updated 2.7 years ago by ★ 1.4k • written 2.7 years ago by ▴ 20
3
votes
8
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5.5k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 3.7 years ago by ▴ 10
3
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5
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2.5k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
3
votes
6
replies
2.2k
views
One-tailed test edgeR possible?
one-tailed edgeR DifferentialExpression test
written 3.2 years ago by • 0
3
votes
5
replies
7.9k
views
How does edgeR calculate fold change?
DifferentialExpression DEA FC FoldChange edgeR
4.4 years ago zhxiaokang ▴ 20
3
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1
reply
944
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 2.0 years ago by 53k • written 2.0 years ago by • 0
3
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3
replies
1.6k
views
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
limma DifferentialExpression
3.9 years ago nhaus ▴ 70
3
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5
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3.7k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 19 months ago by • 0 • written 22 months ago by ▴ 60
3
votes
7
replies
2.9k
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
3
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6
replies
1.0k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 8 weeks ago by • 0
3
votes
6
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1.9k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 5.1 years ago by 43k • written 5.1 years ago by ▴ 50
3
votes
3
replies
1.1k
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
2
votes
3
replies
1.2k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 23 months ago by 68k • written 23 months ago by • 0
2
votes
2
replies
311
views
Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
8 weeks ago jamie.gearing ▴ 60
2
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3
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2.2k
views
DESeq2 extracting relevant contrasts with interactions
DESeq2 DifferentialExpression
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
2
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2
replies
1.7k
views
edgeR: How to display/plot individual miRNAs found to be differentialy expressed?
miRNAData miRNA DifferentialExpression edgeR
3.7 years ago Sarah • 0
2
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2
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1.8k
views
Complex contrasts in limma
RNASeq limma DifferentialExpression
3.9 years ago tcalvo ▴ 100
2
votes
2
replies
1.9k
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by ▴ 20
2
votes
5
replies
1.2k
views
Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 18 months ago by 68k • written 18 months ago by • 0
2
votes
2
replies
9.7k
views
Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 4.3 years ago by ★ 5.0k • written 4.3 years ago by ▴ 10
2
votes
4
replies
2.0k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
4.4 years ago mbenegas ▴ 10
2
votes
1
reply
798
views
Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 23 months ago by 43k • written 23 months ago by ▴ 20
2
votes
3
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2.5k
views
Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter DifferentialExpression Housekeeping DESeq2 NanoString
updated 4.0 years ago by 43k • written 4.0 years ago by • 0
2
votes
4
replies
1.3k
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 2.0 years ago by 53k • written 2.1 years ago by • 0
2
votes
7
replies
5.5k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 2.4 years ago by • 0 • written 4.7 years ago by ▴ 20
2
votes
8
replies
3.1k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
4.7 years ago • updated 4.6 years ago Jane ▴ 10
201 results • Page 1 of 5
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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