Showing : DifferentialExpression • reset
12
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13
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10k
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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
6
votes
11
replies
1.9k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
23 months ago mohammedtoufiq91 ▴ 10
6
votes
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
6
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3
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1.8k
views
differential gene expression
limma differentialexpression
updated 10.3 years ago by ▴ 760 • written 10.3 years ago by ▴ 20
6
votes
5
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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
5
votes
6
replies
953
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 9 months ago by ★ 4.6k • written 9 months ago by ▴ 70
5
votes
2
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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
5
votes
6
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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
5
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6
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1.1k
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
12 months ago Shaimaa Gamal • 0
5
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9
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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
5
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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
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
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
4
votes
6
replies
1.2k
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 11 months ago by 52k • written 12 months ago by • 0
4
votes
10
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1.7k
views
Paired Time course Experiment Design on edgeR between and within groups
edgeR diffcyt limma DifferentialExpression
4.2 years ago Hajar • 0
4
votes
3
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1.5k
views
Limma/voom analysis of time-series data (with only 1 condition)
limma DifferentialExpression
updated 3.0 years ago by 67k • written 3.0 years ago by • 0
4
votes
3
replies
779
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 11 months ago by 52k • written 11 months ago by • 0
3
votes
2
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624
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
11 months ago Shaimaa Gamal • 0
3
votes
6
replies
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
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
3
votes
3
replies
806
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 16 months ago by 67k • written 16 months ago by • 0
3
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3
replies
575
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 9 weeks ago by 52k • written 9 weeks ago by • 0
3
votes
3
replies
1.3k
views
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
limma DifferentialExpression
2.9 years ago nhaus ▴ 70
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
3
votes
3
replies
1.5k
views
Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
DifferentialExpression DESeq2
updated 20 months ago by ★ 1.4k • written 20 months ago by ▴ 20
3
votes
8
replies
4.5k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 2.7 years ago by ▴ 10
3
votes
3
replies
852
views
the count matrix have decimal values
DESeq2 DifferentialExpression
updated 5 months ago by 67k • written 5 months ago by • 0
3
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6
replies
1.8k
views
One-tailed test edgeR possible?
one-tailed edgeR DifferentialExpression test
written 2.2 years ago by • 0
3
votes
5
replies
6.4k
views
How does edgeR calculate fold change?
DifferentialExpression DEA FC FoldChange edgeR
3.4 years ago zhxiaokang ▴ 20
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
3
votes
5
replies
1.2k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
3
votes
7
replies
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
3
votes
6
replies
1.6k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 4.2 years ago by 43k • written 4.2 years ago by ▴ 50
3
votes
1
reply
621
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 12 months ago by 52k • written 12 months ago by • 0
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
2
votes
3
replies
726
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 months ago by 67k • written 11 months ago by • 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
2
votes
2
replies
1.3k
views
edgeR: How to display/plot individual miRNAs found to be differentialy expressed?
miRNAData miRNA DifferentialExpression edgeR
2.7 years ago Sarah • 0
2
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2
replies
1.5k
views
Complex contrasts in limma
RNASeq limma DifferentialExpression
2.9 years ago tcalvo ▴ 100
2
votes
2
replies
1.3k
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 21 months ago by ★ 4.6k • written 21 months ago by ▴ 30
2
votes
5
replies
685
views
Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 6 months ago by 67k • written 6 months ago by • 0
2
votes
2
replies
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
2
votes
4
replies
1.6k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
3.5 years ago mbenegas ▴ 10
2
votes
1
reply
485
views
Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 11 months ago by 43k • written 11 months ago by ▴ 20
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
votes
4
replies
915
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 12 months ago by 52k • written 13 months ago by • 0
2
votes
7
replies
4.2k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 17 months ago by • 0 • written 3.8 years ago by ▴ 20
2
votes
8
replies
2.6k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.7 years ago Jane ▴ 10
2
votes
8
replies
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
votes
2
replies
2.0k
views
DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
3.6 years ago SUMIT • 0
50 results • Page 1 of 1
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Answer: WGCNA sample-data preprocessing order by ATpoint ★ 4.6k
Hi, WGCNA is not a Bioconductor package, please read the documentation to get guidance. See https://support.bioconductor.org/p/9155561/. …
Answer: WGCNA: Can we use high power (26) for signed network? by ATpoint ★ 4.6k
Hi, WGCNA is not a Bioconductor package, please read the documentation to get guidance. See https://support.bioconductor.org/p/9155561/. C…
Answer: Ph.D. scholar by ATpoint ★ 4.6k
Hi, WGCNA is not a Bioconductor package, please read the documentation to get guidance. See https://support.bioconductor.org/p/9155561/. C…
Comment: Recount3 data correspond to TCGA data by Fep29 • 0
Hi, This the solution to mapping TCGA ids in Recount3 to the ids used in the TCGA barcodes: library(recount3) human_projects <- …
Answer: Unable to find sample sheet file for ChAMP methylation data analysis by James W. MacDonald 67k
There is an example file in the extdata directory of the `minfiData` package that you could emulate.
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Answer: DESeq2- merging technical vs biological replicates
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How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
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