Showing : DifferentialExpression • reset
9
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6.8k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 3 months ago by ★ 4.1k • written 2.2 years ago by ▴ 30
6
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11
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1.4k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
15 months ago mohammedtoufiq91 ▴ 10
6
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3
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1.6k
views
differential gene expression
limma differentialexpression
updated 9.7 years ago by ▴ 760 • written 9.7 years ago by ▴ 20
5
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6
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609
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
4 months ago • updated 3 months ago Shaimaa Gamal • 0
5
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3
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743
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 7 weeks ago by 50k • written 8 weeks ago by ▴ 50
5
votes
6
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462
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by ▴ 30
5
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6
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1.7k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.3 years ago by ★ 28k • written 3.3 years ago by • 0
5
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2
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2.3k
views
Query regarding the use of eBayes + topTable and treat + topTreat
Microarray limma DifferentialExpression
updated 21 months ago by 50k • written 2.8 years ago by ▴ 10
5
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9
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1.6k
views
Time series DE gene analysis with edgeR where specific timepoints have NA levels across different patients
edgeR RNASeq DifferentialExpression TimeCourse
updated 2.8 years ago by 65k • written 2.8 years ago by ▴ 830
4
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4
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7.5k
views
DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 2.1 years ago by • 0 • written 2.7 years ago by • 0
4
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5
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1.7k
views
What to do if covariates in design matrix of limma are confounded
limma DifferentialExpression
updated 2.0 years ago by • 0 • written 2.2 years ago by ▴ 30
4
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10
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1.4k
views
Paired Time course Experiment Design on edgeR between and within groups
edgeR diffcyt limma DifferentialExpression
3.6 years ago Hajar • 0
4
votes
3
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385
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 3 months ago by 50k • written 3 months ago by • 0
4
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3
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1.2k
views
Limma/voom analysis of time-series data (with only 1 condition)
limma DifferentialExpression
updated 2.3 years ago by 65k • written 2.3 years ago by • 0
4
votes
2
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1.8k
views
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
DESeq2 SpikeIn Normalization DifferentialExpression
updated 15 months ago by ★ 4.1k • written 15 months ago by ▴ 10
4
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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 9.6 years ago by 42k • written 9.6 years ago by ▴ 90
4
votes
6
replies
653
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 4 months ago by • 0
3
votes
1
reply
331
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 4 months ago by 50k • written 4 months ago by • 0
3
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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
4.6 years ago • updated 2.3 years ago hermidalc ▴ 20
3
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7
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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
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8
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3.4k
views
DESeq2 how to specify contrast to test difference of differences
DifferentialExpression contrasts interaction DESeq2
written 2.1 years ago by ▴ 10
3
votes
3
replies
982
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Subsetting DESeq data set to compare treatments within one group (multi-group experiment)
DifferentialExpression DESeq2
updated 12 months ago by ★ 1.4k • written 12 months ago by ▴ 20
3
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6
replies
1.3k
views
do I have to do this step in creating DGEList ?
DifferentialExpression
updated 14 months ago by 50k • written 14 months ago by • 0
3
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2
replies
322
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
3 months ago Shaimaa Gamal • 0
3
votes
5
replies
4.9k
views
How does edgeR calculate fold change?
DifferentialExpression DEA FC FoldChange edgeR
2.7 years ago zhxiaokang ▴ 20
3
votes
7
replies
1.6k
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 18 months ago by 50k • written 18 months ago by • 0
3
votes
4
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1.4k
views
How to make design matrices or compare contrast in limma
designmatrices differentialexpression makeContrasts limma model.matrix
2.1 years ago mohammedtoufiq91 ▴ 10
3
votes
4
replies
520
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 10 weeks ago by 50k • written 10 weeks ago by ▴ 50
3
votes
6
replies
1.4k
views
One-tailed test edgeR possible?
one-tailed edgeR DifferentialExpression test
written 18 months ago by • 0
3
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3
replies
596
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 8 months ago by 65k • written 8 months ago by • 0
3
votes
6
replies
1.3k
views
Different contrast coding strategies in DESeq2 produce slightly different output?
DESeq2 RNASeqData DifferentialExpression
updated 3.5 years ago by 42k • written 3.5 years ago by ▴ 50
2
votes
6
replies
1000
views
How to update a package at Bioconductor
diffGeneAnalysis DifferentialExpression
updated 11 months ago by 3.9k • written 12 months ago by • 0
2
votes
3
replies
392
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
2
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2
replies
1.1k
views
Complex contrasts in limma
RNASeq limma DifferentialExpression
2.2 years ago tcalvo ▴ 90
2
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3
replies
1.4k
views
DESeq2 extracting relevant contrasts with interactions
DESeq2 DifferentialExpression
updated 3.2 years ago by 42k • written 3.2 years ago by • 0
2
votes
2
replies
1.7k
views
DESeq2 - one groups with no replicates
DESeq2 rnaseqGene DifferentialExpression GeneExpression
2.9 years ago SUMIT • 0
2
votes
2
replies
911
views
Error in checkFullRank(modelMatrix)
DESeq2 BatchEffect DifferentialExpression
updated 13 months ago by ★ 4.1k • written 13 months ago by ▴ 30
2
votes
7
replies
3.0k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.1 years ago by ▴ 20
2
votes
4
replies
552
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 4 months ago by 50k • written 5 months ago by • 0
2
votes
1
reply
237
views
Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 3 months ago by 42k • written 3 months ago by ▴ 20
2
votes
2
replies
963
views
edgeR: How to display/plot individual miRNAs found to be differentialy expressed?
miRNAData miRNA DifferentialExpression edgeR
2.0 years ago Sarah • 0
2
votes
4
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1.2k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
2.8 years ago mbenegas ▴ 10
2
votes
3
replies
1.6k
views
Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
NanoNormIter DifferentialExpression Housekeeping DESeq2 NanoString
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
2
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8
replies
2.1k
views
DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.0 years ago Jane ▴ 10
2
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6
replies
802
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 7 months ago by 16k • written 7 months ago by • 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
4
replies
838
views
Calculated contrasts in DESeq2: difference between manual coefficients and DESeq2 authomatic contrast
DESeq2 DifferentialExpression
updated 16 months ago by 42k • written 16 months ago by • 0
2
votes
3
replies
941
views
Including squared covariates to account for non-linear dependencies in differential gene expression analysis
limma DifferentialExpression
2.2 years ago nhaus ▴ 30
2
votes
2
replies
1.4k
views
Why does limma want log2 intensities but DESeq2 use raw counts?
limma DifferentialExpression DESeq2
3.0 years ago tjbencomo • 0
2
votes
2
replies
6.9k
views
Deseq2 and log2foldchange cutoffs- How to get differentially expressed genes?
DifferentialExpression GeneExpression DESeq2 R
updated 2.6 years ago by ★ 4.1k • written 2.6 years ago by ▴ 10
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Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 65k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 65k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 65k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat by minardsmitha ▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons by boczniak767 ▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
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