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
0
votes
8
replies
846
views
Quickly calculating adjusted Fold Change with DESeq2
DifferentialExpression DESeq2
6 months ago Luca • 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
2
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7
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425
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
13 days ago • updated 10 days ago sajadahmad41454 • 0
2
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7
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3.0k
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EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.1 years ago by ▴ 20
0
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6
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814
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Questionable limma results for differential expression on RNA-seq
RNASeqData DifferentialExpression limma
updated 10 months ago by 50k • written 10 months ago by • 0
4
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6
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657
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 4 months ago by • 0
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
5
votes
6
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464
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 5 weeks ago by ★ 4.1k • written 6 weeks ago by ▴ 30
2
votes
6
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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
5
votes
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
0
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5
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647
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
2
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4
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553
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 4 months ago by 50k • written 5 months ago by • 0
0
votes
4
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330
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
11 weeks ago mperalc • 0
0
votes
4
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759
views
problem while retriving the genes by using p value and log2fc as conditions
Bioconductor Transcriptomics DifferentialExpression DESeq2
12 months ago sreeshmaraj72 • 0
1
vote
4
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590
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
3
votes
4
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530
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
2
votes
4
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729
views
Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
RNASeqData DifferentialExpression SmallRNAData DESeq2
7 months ago Shihui • 0
1
vote
3
replies
263
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 6 days ago by 50k • written 7 days ago by • 0
5
votes
3
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746
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
0
votes
3
replies
138
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 6 days ago by 42k • written 6 days ago by • 0
2
votes
3
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393
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 66k • written 3 months ago by • 0
4
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3
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387
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 3 months ago by 50k • written 3 months ago by • 0
1
vote
3
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616
views
Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 5 months ago by • 0
0
votes
3
replies
682
views
limma paired design
DifferentialExpression limma
updated 11 months ago by 66k • written 11 months ago by • 0
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
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
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
1
vote
3
replies
596
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
0
votes
3
replies
283
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 20 days ago by 66k • written 22 days ago by • 0
0
votes
3
replies
230
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 19 days ago by ★ 4.1k • written 19 days ago by • 0
1
vote
3
replies
445
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
1
vote
2
replies
252
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
8 weeks ago • updated 7 weeks ago Chanderkant Chaudhary • 0
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
3
votes
2
replies
323
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
3 months ago Shaimaa Gamal • 0
0
votes
2
replies
250
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 5 weeks ago by 42k • written 6 weeks ago by ▴ 30
0
votes
2
replies
536
views
RSubread DESeq2
RNASeqData DifferentialExpression DESeq2
8 months ago Beyza • 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
0
votes
2
replies
711
views
Correct DESeq2 design for tumoral stage differences in tumoral and matched-normal samples
DifferentialExpression RNASeq DESeq2
10 months ago Matteo • 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
2
replies
305
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
0
votes
2
replies
184
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 6 weeks ago by 66k • written 6 weeks ago by • 0
0
votes
2
replies
332
views
PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 3 months ago by 42k • 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
1
vote
1
reply
554
views
NA p values in edgeR results
DifferentialExpression edgeR
updated 10 months ago by 50k • written 10 months ago by • 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
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
1
reply
416
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
0
votes
1
reply
187
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 11 days ago by ★ 4.1k • written 11 days ago by • 0
50 results • Page 1 of 1
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Answer: Documenting resources in an `ExperimentHub` package? by James W. MacDonald 66k
The easiest way to do that IMO is to use emacs/ESS (or I believe there is some newfangled thing called RStudio? Not personally familiar, bu…
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We are still waiting for the goseq to respond to our requests but will take action next week if it is not resolved. ChAMP is currently una…
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Hello everyone, I am new on this site but not a noob in R (I guess). I am facing the same problem. For me, it depends on the NOIseq plot fu…
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Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data by James W. MacDonald 66k
Yes, you can use `limma`.
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how to control age and gender effect in expression data using DESeq2
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