Showing : DifferentialExpression • reset
12
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GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 11 months ago by ★ 4.6k • written 2.9 years ago by ▴ 70
5
votes
4
replies
9.7k
views
DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 2.8 years ago by • 0 • written 3.4 years ago by ▴ 10
2
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2
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7.9k
views
Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 3.3 years ago by ★ 4.6k • written 3.3 years ago by ▴ 10
4
votes
2
replies
7.1k
views
DESeq2: removing levels from a factor or not having them in the analysis at all
deseq2 differentialexpression
updated 10.3 years ago by 43k • written 10.3 years ago by ▴ 110
1
vote
3
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6.4k
views
Manually calculating log2 fold change values from DESeq2 normalized counts
DESeq2 DifferentialExpression
2.1 years ago Jayesh Kumar • 0
3
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5
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6.4k
views
How does edgeR calculate fold change?
DifferentialExpression DEA FC FoldChange edgeR
3.4 years ago zhxiaokang ▴ 20
3
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8
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4.5k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 2.7 years ago by ▴ 10
2
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7
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4.2k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 17 months ago by • 0 • written 3.8 years ago by ▴ 20
0
votes
7
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3.3k
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topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange topGO DifferentialExpression enrichment
updated 4.2 years ago by 52k • written 4.2 years ago by ▴ 20
0
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3
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3.1k
views
Comparisons both between and within subjects using DESeq2
deseq2 edger differentialexpression
10.3 years ago asaferali • 0
6
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2
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3.1k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 24 months ago by ★ 4.6k • written 24 months ago by ▴ 10
1
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1
reply
3.1k
views
Limma interaction term
RNASeqData limma DifferentialExpression
updated 2.9 years ago by 52k • written 2.9 years ago by • 0
5
votes
2
replies
3.0k
views
Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 2.4 years ago by 52k • written 3.4 years ago by ▴ 10
3
votes
6
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2.6k
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
5.3 years ago • updated 3.0 years ago hermidalc ▴ 20
2
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8
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2.6k
views
Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression DESeq2
written 19 months ago by ▴ 10
2
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8
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2.6k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.7 years ago Jane ▴ 10
0
votes
2
replies
2.5k
views
Using DESeq2 for Differential Expression Analysis with Interaction Term
DifferentialExpression GeneExpression DESeq2 Design()
3.3 years ago p.l.chen • 0
1
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2
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2.4k
views
unbalanced cell count and unbalanced read count across samples in pseudobulk differential expression analysis using scRNA-seq data
scRNAseq DifferentialExpression DESeq2
2.8 years ago Ismail • 0
1
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8
replies
2.3k
views
DESeq2 analysis for targeted RNA-seq
DifferentialExpression DESeq2
3.0 years ago dadca596 • 0
3
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7
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2.3k
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 2.2 years ago by 52k • written 2.2 years ago by • 0
0
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2
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2.3k
views
Limma Differential Analysis on Proteomics data
Proteomics limma Limma DifferentialExpression
updated 3.0 years ago by 52k • written 3.0 years ago by • 0
5
votes
6
replies
2.2k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.9 years ago by ★ 28k • written 4.0 years ago by • 0
2
votes
2
replies
2.2k
views
Normal Patient Samples from GSE62944
GSE62944 annotationhub differentialexpression
updated 8.8 years ago by ▴ 390 • written 8.8 years ago by • 0
4
votes
5
replies
2.1k
views
What to do if covariates in design matrix of limma are confounded
limma DifferentialExpression
updated 2.7 years ago by • 0 • written 2.9 years ago by ▴ 70
0
votes
5
replies
2.1k
views
Weird output of DESeq2 when using single sample from one group agains the other group (6 samples), really need some help
DifferentialExpression DESeq2
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 10
2
votes
3
replies
2.1k
views
Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter DifferentialExpression Housekeeping DESeq2 NanoString
updated 3.0 years ago by 43k • written 3.0 years ago by • 0
2
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2
replies
2.0k
views
DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
3.6 years ago SUMIT • 0
1
vote
8
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2.0k
views
edgeR design matrix with multiple cell types and combination treatments
DifferentialExpression celltype treatment edgeR limma
2.6 years ago giBio • 0
0
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1
reply
2.0k
views
TCC::ERROR: Need the design matrix for GLM.
DifferentialExpression Normalization Cancer edgeR baySeq DESeq EBSeq TCC Normalization
updated 10.8 years ago by ▴ 10 • written 10.8 years ago by ▴ 100
5
votes
9
replies
2.0k
views
Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 3.5 years ago by 67k • written 3.5 years ago by ▴ 840
3
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6
replies
1.9k
views
do I have to do this step in creating DGEList ?
DifferentialExpression
updated 23 months ago by 52k • written 23 months ago by • 0
6
votes
5
replies
1.9k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 12 weeks ago by 52k • written 10 months ago by ▴ 50
3
votes
5
replies
1.9k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 7 months ago by • 0 • written 10 months ago by ▴ 50
6
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11
replies
1.9k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
23 months ago mohammedtoufiq91 ▴ 10
0
votes
8
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1.9k
views
Three conditions and two time points
DifferentialExpression DESeq2 time
3.3 years ago • updated 3.2 years ago AZ ▴ 30
3
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6
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1.8k
views
One-tailed test edgeR possible?
one-tailed edgeR DifferentialExpression test
written 2.2 years ago by • 0
0
votes
1
reply
1.8k
views
TCC::ERROR: Need the design matrix for GLM
DifferentialExpression Normalization Cancer edgeR baySeq DESeq EBSeq TCC Normalization
updated 10.8 years ago by ▴ 10 • written 10.8 years ago by 52k
0
votes
2
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1.8k
views
Comparison when Control is in differen batch
DESeq2 DifferentialExpression
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by ▴ 30
6
votes
3
replies
1.8k
views
differential gene expression
limma differentialexpression
updated 10.3 years ago by ▴ 760 • written 10.3 years ago by ▴ 20
0
votes
3
replies
1.8k
views
Offsets and normalization in EdgeR
edgeR DifferentialExpression
updated 4.2 years ago by 52k • written 4.2 years ago by • 0
0
votes
7
replies
1.7k
views
DESeq2 on allelic reads
RNASeq DifferentialExpression DESeq2
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
2
votes
2
replies
1.7k
views
Why does limma want log2 intensities but DESeq2 use raw counts?
limma DifferentialExpression DESeq2
3.7 years ago tjbencomo • 0
0
votes
4
replies
1.7k
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
20 months ago ruba-mahmoud • 0
2
votes
3
replies
1.7k
views
DESeq2 extracting relevant contrasts with interactions
DESeq2 DifferentialExpression
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
4
votes
10
replies
1.7k
views
Paired Time course Experiment Design on edgeR between and within groups
edgeR diffcyt limma DifferentialExpression
4.2 years ago Hajar • 0
0
votes
8
replies
1.7k
views
Swish log2FC NA output
swish fishpond DifferentialExpression
2.5 years ago jvandinter • 0
3
votes
4
replies
1.7k
views
How to make design matrices or compare contrast in limma
designmatrices differentialexpression makeContrasts limma model.matrix
2.8 years ago mohammedtoufiq91 ▴ 10
0
votes
2
replies
1.7k
views
How well does "Trinity-Differential-Expression" work on normalized raw counts without RSEM abundance of estimation
Trinity DifferentialExpression RSEM RNAseq edgeR
4.1 years ago harelarik ▴ 60
3
votes
7
replies
1.7k
views
Getting differentially expressed genes for time points
edgeR DifferentialExpression limma
updated 3.9 years ago by 52k • written 3.9 years ago by ▴ 30
0
votes
7
replies
1.6k
views
Help with differential gene expression using Agilent Microarray data (from GEO database)
limma Paireddata DifferentialExpression
updated 2.2 years ago by 67k • written 2.3 years ago by • 0
50 results • Page 1 of 1
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Hi, WGCNA is not a Bioconductor package, please read the documentation to get guidance. See https://support.bioconductor.org/p/9155561/. …
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Hi, This the solution to mapping TCGA ids in Recount3 to the ids used in the TCGA barcodes: library(recount3) human_projects <- …
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There is an example file in the extdata directory of the `minfiData` package that you could emulate.
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