Showing : DifferentialExpression • reset
9
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13
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6.7k
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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
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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
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 • updated 3.5 years ago Hajar • 0
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
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 2.0 years ago by ▴ 10
0
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8
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836
views
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
views
Swish log2FC NA output
swish fishpond DifferentialExpression
21 months ago jvandinter • 0
1
vote
8
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1.6k
views
edgeR design matrix with multiple cell types and combination treatments
DifferentialExpression celltype treatment edgeR limma
23 months ago giBio • 0
1
vote
8
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1.6k
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 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 • updated 2.3 years ago dadca596 • 0
0
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8
replies
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
votes
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
votes
7
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336
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
7 days ago • updated 4 days ago sajadahmad41454 • 0
0
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7
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1.3k
views
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
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
0
votes
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
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
6
replies
989
views
How to update a package at Bioconductor
diffGeneAnalysis DifferentialExpression
updated 10 months ago by 3.9k • written 11 months ago by • 0
5
votes
6
replies
451
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 4 weeks ago by ★ 4.1k • written 5 weeks ago by ▴ 30
4
votes
6
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631
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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1.6k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.2 years ago by ★ 28k • written 3.3 years ago by • 0
0
votes
6
replies
800
views
Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 9 months ago by 50k • written 9 months ago by • 0
3
votes
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
votes
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
votes
6
replies
886
views
DESeq2 time course confusion
DESeq2 DifferentialExpression
2.9 years ago rajpal22288 ▴ 10
5
votes
6
replies
593
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
3 months ago Shaimaa Gamal • 0
3
votes
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
votes
6
replies
792
views
Biostrings error at retrieving protein sequences
SequenceMatching Biostrings DifferentialExpression Proteome
updated 7 months ago by 16k • written 7 months ago by • 0
1
vote
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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637
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
0
votes
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
4.8k
views
How does edgeR calculate fold change?
DifferentialExpression DEA FC FoldChange edgeR
2.7 years ago zhxiaokang ▴ 20
0
votes
5
replies
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 2.0 years ago by • 0 • written 2.2 years ago by ▴ 30
0
votes
4
replies
755
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
11 months ago sreeshmaraj72 • 0
0
votes
4
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319
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 weeks ago • updated 10 weeks ago mperalc • 0
4
votes
4
replies
7.4k
views
DESeq2: LRT or WALD guidance
DESeq2 RNASeq DifferentialExpression
updated 2.1 years ago by • 0 • written 2.7 years ago by • 0
0
votes
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
replies
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
484
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
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4
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1.1k
views
enhanced volcano , different -log10pvalue of the same gene
EnhancedVolcano RNASeqData DifferentialExpression
12 months ago ruba-mahmoud • 0
1
vote
4
replies
940
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
571
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
834
views
Calculated contrasts in DESeq2: difference between manual coefficients and DESeq2 authomatic contrast
DESeq2 DifferentialExpression
updated 15 months ago by 42k • written 16 months ago by • 0
2
votes
4
replies
541
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 4 months ago by 50k • written 4 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 ...
Replies
Comment: error running enricher from clusterprofiler by Yael • 0
It worked!!! Thanks alot, i think something in the gene_list wasnt right... Thanks agian
Comment: Create protein sequences including variants from a VCF file by Yun • 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization? by Daniel • 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Votes
Answer: Trim/Filter out-of-bounds GRanges
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
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