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
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
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
2
votes
6
replies
1.0k
views
How to update a package at Bioconductor
diffGeneAnalysis DifferentialExpression
updated 11 months ago by 3.9k • written 12 months ago by • 0
0
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8
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847
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
6 months ago Luca • 0
0
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6
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814
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
2
votes
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
0
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4
replies
759
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
12 months ago sreeshmaraj72 • 0
5
votes
3
replies
748
views
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
2
votes
4
replies
730
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
7 months ago Shihui • 0
0
votes
2
replies
712
views
Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
10 months ago Matteo • 0
0
votes
3
replies
683
views
limma paired design
DifferentialExpression limma
updated 11 months ago by 66k • written 11 months ago by • 0
4
votes
6
replies
657
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 4 months ago by • 0
0
votes
5
replies
647
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
0
votes
1
reply
617
views
DESeq2 about comparasion of gene expression change on two-time points between two group samples.
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 12 months ago by ★ 1.4k • written 12 months ago by • 0
1
vote
3
replies
616
views
Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 5 months ago by • 0
5
votes
6
replies
609
views
Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
4 months ago Shaimaa Gamal • 0
1
vote
3
replies
598
views
DESeq differential expression results are too stringet. How to relax my criteria
shrinkage DifferentialExpression DESeq2
updated 9 months ago by ★ 4.1k • written 9 months ago by ▴ 10
3
votes
3
replies
596
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 8 months ago by 66k • written 8 months ago by • 0
1
vote
4
replies
591
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
557
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 4 months ago by 50k • written 5 months ago by • 0
1
vote
1
reply
555
views
NA p values in edgeR results
DifferentialExpression edgeR
updated 10 months ago by 50k • written 10 months ago by • 0
0
votes
2
replies
537
views
RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
8 months ago Beyza • 0
3
votes
4
replies
532
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 10 weeks ago by 50k • written 11 weeks ago by ▴ 50
0
votes
1
reply
517
views
Design formula for genotype-specific condition effects using ~group in the design
RNASeqData DifferentialExpression DESeq2
updated 11 months ago by 42k • written 11 months ago by • 0
0
votes
1
reply
517
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
1
vote
0
replies
495
views
WGCNA of two different cohorts study
DifferentialExpression WGCNA
updated 11 months ago by 42k • written 12 months ago by ▴ 20
0
votes
3
replies
470
views
how to adjust other conditions when calling DEGs by DESeq2
DifferentialExpression DESeq2
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
1
vote
2
replies
468
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
5
votes
6
replies
464
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 5 weeks ago by ★ 4.1k • written 6 weeks ago by ▴ 30
0
votes
0
replies
452
views
DEG after deconvolution of GeoMx Spatial data using scRNA-seq reference
GeoMx DifferentialExpression GeomxTools
updated 10 months ago by 66k • written 10 months ago by • 0
1
vote
3
replies
446
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
0
votes
1
reply
442
views
''Model_Matrix'' error
DifferentialExpression limma
updated 8 months ago by 50k • written 8 months ago by • 0
0
votes
3
replies
442
views
DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
2
votes
7
replies
429
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
13 days ago • updated 10 days ago sajadahmad41454 • 0
1
vote
1
reply
420
views
Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
0
votes
1
reply
418
views
Is it possible to use pre-ranked list in EGSEA?
EGSEA EGSEAdata EGSEA123 DifferentialExpression
updated 8 months ago by 66k • written 8 months ago by • 0
2
votes
3
replies
394
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 66k • written 3 months ago by • 0
0
votes
0
replies
390
views
clusterProfiler code to GO enrichment analysis seems to be incomplete
clusterProfiler DifferentialExpression
7 months ago nromerov • 0
4
votes
3
replies
387
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 3 months ago by 50k • written 3 months ago by • 0
0
votes
2
replies
382
views
StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
5 months ago Luca • 0
0
votes
1
reply
374
views
DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 6 months ago by 42k • written 6 months ago by ▴ 10
0
votes
2
replies
349
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 9 weeks ago by 42k • written 9 weeks ago by • 0
0
votes
2
replies
333
views
PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 3 months ago by 42k • written 3 months ago by • 0
3
votes
1
reply
332
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 4 months ago by 50k • written 4 months ago by • 0
0
votes
4
replies
331
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
12 weeks ago • updated 11 weeks ago mperalc • 0
3
votes
2
replies
323
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
3 months ago Shaimaa Gamal • 0
2
votes
1
reply
321
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
0
votes
2
replies
306
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
1
vote
3
replies
285
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 6 weeks ago by 66k • written 6 weeks ago by • 0
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After facing the same problem, I realise that you can direct your plot in the matrix with the *par()* option `par(..., mfg = c(1,2))`. If i…
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how to control age and gender effect in expression data using DESeq2
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