Showing : DifferentialExpression • reset
9
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13
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6.8k
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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
replies
1.4k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
15 months ago mohammedtoufiq91 ▴ 10
4
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10
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1.4k
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Paired Time course Experiment Design on edgeR between and within groups
edgeR diffcyt limma DifferentialExpression
3.6 years ago Hajar • 0
5
votes
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
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
0
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8
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846
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Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
6 months ago Luca • 0
2
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8
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2.1k
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DESeq2 numbers of DEGs not consistent with PCA plot
DifferentialExpression DESeq2 contrasts
3.0 years ago Jane ▴ 10
0
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8
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1.4k
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Swish log2FC NA output
swish fishpond DifferentialExpression
21 months ago jvandinter • 0
1
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8
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1.6k
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edgeR design matrix with multiple cell types and combination treatments
DifferentialExpression celltype treatment edgeR limma
23 months ago giBio • 0
1
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8
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1.6k
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Whether to build DESeq2 model with all data and then contrast groups or subset groups first, build model and then contrast?
DifferentialExpression DESeq2
written 11 months ago by • 0
1
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8
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1.7k
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DESeq2 analysis for targeted RNA-seq
DifferentialExpression DESeq2
2.4 years ago dadca596 • 0
0
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8
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1.5k
views
Three conditions and two time points
DifferentialExpression DESeq2 time
2.6 years ago AZ ▴ 30
3
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7
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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
0
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7
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2.4k
views
topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange topGO DifferentialExpression enrichment
updated 3.5 years ago by 50k • written 3.5 years ago by ▴ 20
0
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7
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1.4k
views
DESeq2 on allelic reads
RNASeq DifferentialExpression DESeq2
updated 2.1 years ago by 42k • written 2.1 years ago by • 0
2
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7
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417
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
12 days ago • updated 9 days ago sajadahmad41454 • 0
0
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7
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1.3k
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Help with differential gene expression using Agilent Microarray data (from GEO database)
limma Paireddata DifferentialExpression
updated 18 months ago by 65k • written 19 months ago by • 0
3
votes
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
0
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7
replies
1.2k
views
Which Limma guide is recommended ?
limma R DifferentialExpression
2.1 years ago • updated 2.0 years ago JAcky • 0
2
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7
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3.0k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.1 years ago by ▴ 20
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
5
votes
6
replies
462
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by ▴ 30
4
votes
6
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654
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 4 months ago by • 0
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
0
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6
replies
812
views
Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 10 months ago by 50k • written 10 months ago by • 0
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
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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6
replies
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
0
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6
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887
views
DESeq2 time course confusion
DESeq2 DifferentialExpression
2.9 years ago rajpal22288 ▴ 10
5
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6
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609
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
4 months ago • updated 3 months ago Shaimaa Gamal • 0
3
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6
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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
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6
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802
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 7 months ago by 16k • written 7 months ago by • 0
1
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6
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1.2k
views
Error while running DESeq2
DifferentialExpression
22 months ago srikar • 0
0
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5
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646
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Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
0
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5
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1.3k
views
DESeq2 shows comparison nonsignificant, unclear why
DESeq2 RNASeq DifferentialExpression
updated 20 months ago by 42k • written 2.7 years ago by • 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
0
votes
5
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1.6k
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 2.3 years ago by 42k • written 2.3 years ago by ▴ 10
4
votes
5
replies
1.7k
views
What to do if covariates in design matrix of limma are confounded
limma DifferentialExpression
updated 2.1 years ago by • 0 • written 2.2 years ago by ▴ 30
0
votes
4
replies
758
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
12 months ago sreeshmaraj72 • 0
0
votes
4
replies
328
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 weeks ago mperalc • 0
4
votes
4
replies
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
0
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4
replies
1.1k
views
Thoughts on how to model gene expression data from two groups in a clinical trial
Microarray DifferentialExpression
23 months ago S • 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
521
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
0
votes
4
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1.2k
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
12 months ago ruba-mahmoud • 0
1
vote
4
replies
946
views
How to figure out the FC value from Limma
limma DEGseq DifferentialExpression
updated 24 months ago by ★ 3.9k • written 24 months ago by • 0
1
vote
4
replies
589
views
rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 6 months ago by 42k • written 6 months ago by ▴ 60
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
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
4
replies
1.2k
views
edgeR output doubts
logFC edgeR DifferentialExpression scRNAseq
2.8 years ago mbenegas ▴ 10
50 results • Page 1 of 1
Recent ...
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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 …
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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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