Showing : DifferentialExpression • reset
9
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13
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6.3k
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GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 10 weeks ago by ★ 4.0k • written 2.1 years ago by ▴ 30
6
votes
3
replies
1.6k
views
differential gene expression
limma differentialexpression
updated 9.6 years ago by ▴ 760 • written 9.6 years ago by ▴ 20
6
votes
11
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1.3k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
14 months ago mohammedtoufiq91 ▴ 10
5
votes
6
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1.6k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.2 years ago by ★ 28k • written 3.2 years ago by • 0
5
votes
6
replies
377
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 6 days ago by ★ 4.0k • written 9 days ago by ▴ 30
5
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9
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1.5k
views
Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 2.7 years ago by 65k • written 2.7 years ago by ▴ 830
5
votes
3
replies
664
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 22 days ago by 50k • written 29 days ago by ▴ 50
5
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2
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2.2k
views
Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 20 months ago by 50k • written 2.7 years ago by ▴ 10
5
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6
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515
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
12 weeks ago Shaimaa Gamal • 0
4
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3
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315
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
4
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2
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1.7k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 14 months ago by ★ 4.0k • written 14 months ago by ▴ 10
4
votes
4
replies
7.1k
views
DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 2.0 years ago by • 0 • written 2.7 years ago by • 0
4
votes
5
replies
1.7k
views
What to do if covariates in design matrix of limma are confounded
limma DifferentialExpression
updated 23 months ago by • 0 • written 2.2 years ago by ▴ 30
4
votes
6
replies
539
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 10 weeks ago by 50k • written 3 months ago by • 0
4
votes
2
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6.7k
views
DESeq2: removing levels from a factor or not having them in the analysis at all
deseq2 differentialexpression
updated 9.5 years ago by 41k • written 9.5 years ago by ▴ 90
4
votes
10
replies
1.3k
views
Paired Time course Experiment Design on edgeR between and within groups
edgeR diffcyt limma DifferentialExpression
3.5 years ago Hajar • 0
4
votes
3
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1.2k
views
Limma/voom analysis of time-series data (with only 1 condition)
limma DifferentialExpression
updated 2.2 years ago by 65k • written 2.2 years ago by • 0
3
votes
1
reply
248
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 3 months ago by 50k • written 3 months ago by • 0
3
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3
replies
556
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 7 months ago by 65k • written 7 months ago by • 0
3
votes
7
replies
1.4k
views
Getting differentially expressed genes for time points
edgeR DifferentialExpression limma
updated 3.2 years ago by 50k • written 3.2 years ago by ▴ 30
3
votes
6
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2.2k
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
4.5 years ago • updated 2.2 years ago hermidalc ▴ 20
3
votes
4
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1.3k
views
How to make design matrices or compare contrast in limma
designmatrices differentialexpression makeContrasts limma model.matrix
2.0 years ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
929
views
Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
DifferentialExpression DESeq2
updated 11 months ago by ★ 1.3k • written 11 months ago by ▴ 20
3
votes
8
replies
3.3k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 23 months ago by ▴ 10
3
votes
6
replies
1.2k
views
do I have to do this step in creating DGEList ?
DifferentialExpression
updated 13 months ago by 50k • written 13 months ago by • 0
3
votes
4
replies
372
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 6 weeks ago by 50k • written 6 weeks ago by ▴ 50
3
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5
replies
4.6k
views
How does edgeR calculate fold change?
DifferentialExpression DEA FC FoldChange edgeR
2.6 years ago zhxiaokang ▴ 20
3
votes
2
replies
259
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
10 weeks ago Shaimaa Gamal • 0
3
votes
6
replies
1.3k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 3.4 years ago by 41k • written 3.4 years ago by ▴ 50
3
votes
6
replies
1.4k
views
One-tailed test edgeR possible?
one-tailed edgeR DifferentialExpression test
written 17 months ago by • 0
3
votes
7
replies
1.5k
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 17 months ago by 50k • written 17 months ago by • 0
2
votes
2
replies
1.6k
views
DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
2.8 years ago SUMIT • 0
2
votes
6
replies
936
views
How to update a package at Bioconductor
diffGeneAnalysis DifferentialExpression
updated 10 months ago by 3.8k • written 11 months ago by • 0
2
votes
2
replies
1.0k
views
Complex contrasts in limma
RNASeq limma DifferentialExpression
2.1 years ago tcalvo ▴ 90
2
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3
replies
1.4k
views
DESeq2 extracting relevant contrasts with interactions
DESeq2 DifferentialExpression
updated 3.1 years ago by 41k • written 3.2 years ago by • 0
2
votes
4
replies
797
views
Calculated contrasts in DESeq2: difference between manual coefficients and DESeq2 authomatic contrast
DESeq2 DifferentialExpression
updated 15 months ago by 41k • written 15 months ago by • 0
2
votes
3
replies
333
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
2
votes
2
replies
845
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 12 months ago by ★ 4.0k • written 12 months ago by ▴ 30
2
votes
7
replies
2.9k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 7 months ago by • 0 • written 3.0 years ago by ▴ 20
2
votes
1
reply
201
views
Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 10 weeks ago by 41k • written 11 weeks ago by ▴ 20
2
votes
2
replies
6.7k
views
Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 2.5 years ago by ★ 4.0k • written 2.5 years ago by ▴ 10
2
votes
2
replies
1.3k
views
Why does limma want log2 intensities but DESeq2 use raw counts?
limma DifferentialExpression DESeq2
2.9 years ago tjbencomo • 0
2
votes
4
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1.2k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
2.7 years ago mbenegas • 0
2
votes
3
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1.5k
views
Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter DifferentialExpression Housekeeping DESeq2 NanoString
updated 2.2 years ago by 41k • written 2.2 years ago by • 0
2
votes
6
replies
745
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 6 months ago by 16k • written 6 months ago by • 0
2
votes
2
replies
911
views
edgeR: How to display/plot individual miRNAs found to be differentialy expressed?
miRNAData miRNA DifferentialExpression edgeR
23 months ago Sarah • 0
2
votes
2
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1.9k
views
Normal Patient Samples from GSE62944
GSE62944 annotationhub differentialexpression
updated 8.1 years ago by ▴ 390 • written 8.1 years ago by • 0
2
votes
3
replies
886
views
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
limma DifferentialExpression
2.1 years ago nhaus ▴ 30
2
votes
8
replies
2.0k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
2.9 years ago Jane ▴ 10
2
votes
4
replies
474
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 3 months ago by 50k • written 4 months ago by • 0
50 results • Page 1 of 1
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Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0
Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…
Comment: Finding DEGs by using edgeR by prity6459 • 0
Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …
Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k
It doesn't seem to me that there is necessarily any problem with the analysis. You that there are "too many low-reads" but actually there …
Answer: How to make DGEList and design matrix by edgeR package by Gordon Smyth 50k
Your question is curious because you showed code that made a DGEList and design matrix in your previous post just 15 hours ago. Please h…
Answer: Finding DEGs by using edgeR by Gordon Smyth 50k
I am not clear what you mean that you have already normalized your data. How exactly did you normalize the data? The best way to do an edg…
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Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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