Showing : differentialexpression • reset
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
6 days ago • updated 1 day ago abadgerw • 0
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165
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
6 days ago • updated 1 day ago abadgerw • 0
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159
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 20 days ago by 42k • written 5 weeks ago by • 0
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3
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 12 weeks ago by 51k • written 12 weeks ago by • 0
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638
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 3 months ago by 67k • written 3 months ago by • 0
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468
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 3 months ago by • 0
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5
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884
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 3 months ago by ★ 1.4k • written 3 months ago by • 0
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3
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549
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Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 3 months ago by ★ 4.5k • written 3 months ago by • 0
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 3 months ago by 67k • written 4 months ago by • 0
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376
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
4 months ago nhaus ▴ 70
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 4 months ago by • 0 • written 8 months ago by ▴ 50
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411
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 5 months ago by 67k • written 5 months ago by ▴ 70
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570
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
5 months ago vohara4 • 0
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338
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How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 5 months ago by 67k • written 5 months ago by • 0
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 6 months ago by 42k • written 6 months ago by • 0
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603
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 6 months ago by 51k • written 6 months ago by • 0
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365
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 6 months ago by ★ 4.5k • written 6 months ago by • 0
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7
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
6 months ago sajadahmad41454 • 0
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 6 months ago by ★ 4.5k • written 6 months ago by • 0
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3
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Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 6 months ago by 67k • written 6 months ago by • 0
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483
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 7 months ago by 42k • written 7 months ago by ▴ 70
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843
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 7 months ago by ★ 4.5k • written 7 months ago by ▴ 70
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 7 months ago by 67k • written 7 months ago by • 0
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2
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422
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 7 months ago by 67k • written 7 months ago by • 0
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479
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
7 months ago Chanderkant Chaudhary • 0
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5
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1.6k
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 16 days ago by 51k • written 7 months ago by ▴ 50
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 months ago by 51k • written 8 months ago by • 0
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619
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 8 months ago by 42k • written 8 months ago by • 0
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702
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 9 months ago by • 0
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4
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639
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
8 months ago mperalc • 0
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485
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
9 months ago Abril • 0
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 9 months ago by ★ 4.5k • written 9 months ago by • 0
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557
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
9 months ago Shaimaa Gamal • 0
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676
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 9 months ago by 51k • written 9 months ago by • 0
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3
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650
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 9 months ago by 67k • written 9 months ago by • 0
2
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1
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432
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 9 months ago by 42k • written 9 months ago by ▴ 20
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529
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PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 9 months ago by 42k • written 9 months ago by • 0
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6
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950
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
9 months ago Shaimaa Gamal • 0
4
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6
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1.0k
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 9 months ago by 51k • written 10 months ago by • 0
3
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1
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578
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Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 10 months ago by 51k • written 10 months ago by • 0
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882
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Read Count Normalisation and validation of analysis
DifferentialExpression DESeq2
written 10 months ago by • 0
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5
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980
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Help with model for differential expression analysis
DifferentialExpression edgeR
10 months ago • updated 9 months ago Lucy ▴ 60
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689
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DESeq with multiple condition
MoleculeExperiment DifferentialExpression DESeq2
updated 10 months ago by ★ 4.5k • written 10 months ago by • 0
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1
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622
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Deseq2 -Model matrix not full rank error: A complex case
RNASeqData DifferentialExpression DESeq2
updated 10 months ago by ★ 4.5k • written 10 months ago by • 0
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4
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845
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Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 10 months ago by 51k • written 11 months ago by • 0
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694
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StringDB: Cannot use payload mechanism to colour nodes
RNASeqData STRINGdb DifferentialExpression GraphAndNetwork Network
11 months ago Luca • 0
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 11 months ago by 51k • written 11 months ago by • 0
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526
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DESeq2 and determining effects of treatment on a priori/candidate genes from a bulk-RNAseq experiment
RNASeqData DifferentialExpression DESeq2
updated 12 months ago by 42k • written 12 months ago by ▴ 10
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4
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824
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rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 12 months ago by 42k • written 12 months ago by ▴ 60
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by Robert Castelo ★ 3.4k
Hi, this is a long comment thread on 4-year old post, please open a new post with you question. To increase the odds of getting useful answ…
Answer: DESeq2 rerun returns different results by ATpoint ★ 4.5k
DESeq2 is deterministic if you use same input, code and software versions. Make sure to version-control your environment by at least tracki…
Answer: [How to construct a model.matrix ] by Gordon Smyth 51k
> Initially, I simply used > `lm(Epigenetic_age ~ Age_group + Age + Sex + PC1 + PC2 + PC3 + PC4 + PC5 + B + CD4T + CD8T + Mono + NK + Neutr…
Comment: How to extract phastcons score for all protein coding genes and lncRNAs using Ge by rania.alanany • 0
Hi Robert, Thank you for the explanation, But I am still little bit confused, Is the annotation package (TxDb.Hsapiens.UCSC.hg38.knownGene)…
Comment: Merge Replicates vs Mixed Model by abadgerw • 0
@gabrielhoffman any insight?
Votes
A: Some questions for remove batch effect by using mnnCorrect
A: Recommendations for combining multiple 10x runs into one SingleCellExperiment
Answer: [How to construct a model.matrix ]
Answer: Handling biological replicates in DESeq2
Comment: biomaRt rnorvegicus_gene_ensembl not available anymore
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