Showing : DifferentialExpression • reset
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Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 12 days ago by ★ 4.8k • written 12 days ago by • 0
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8
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2.5k
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
18 days ago • updated 15 days ago ktz • 0
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3
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613
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 8 weeks ago by 43k • written 9 weeks ago by • 0
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1
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186
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
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1
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278
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 11 weeks ago by 43k • written 12 weeks ago by • 0
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5
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417
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 3 months ago by • 0
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2
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430
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
4 months ago Tadeoye ▴ 20
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9
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1.2k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 4 months ago by 68k • written 4 months ago by • 0
3
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3
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689
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 5 months ago by 52k • written 5 months ago by • 0
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3
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595
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
5 months ago • updated 4 months ago abadgerw • 0
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5
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874
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
5 months ago • updated 4 months ago abadgerw • 0
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1
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322
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 6 months ago by 43k • written 6 months ago by • 0
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6
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1.1k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 5 months ago by 43k • written 6 months ago by • 0
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3
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723
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 8 months ago by 52k • written 8 months ago by • 0
3
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3
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1.2k
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 8 months ago by 68k • written 8 months ago by • 0
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3
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771
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 8 months ago by • 0
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5
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1.8k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 8 months ago by ★ 1.4k • written 8 months ago by • 0
0
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3
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743
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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 9 months ago by ★ 4.8k • written 9 months ago by • 0
2
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5
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838
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 9 months ago by 68k • written 9 months ago by • 0
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0
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596
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
9 months ago nhaus ▴ 70
3
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5
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2.6k
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 10 months ago by • 0 • written 13 months ago by ▴ 60
2
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1
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624
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 10 months ago by 68k • written 10 months ago by ▴ 70
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4
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820
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
10 months ago vohara4 • 0
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1
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475
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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 10 months ago by 68k • written 10 months ago by • 0
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3
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561
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 11 months ago by 43k • written 11 months ago by • 0
1
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3
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837
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 11 months ago by 52k • written 11 months ago by • 0
0
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1
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495
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 11 months ago by ★ 4.8k • written 11 months ago by • 0
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7
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1.5k
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
11 months ago sajadahmad41454 • 0
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3
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1.1k
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 11 months ago by ★ 4.8k • written 11 months ago by • 0
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3
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693
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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 11 months ago by 68k • written 11 months ago by • 0
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2
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649
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 12 months ago by 43k • written 12 months ago by ▴ 70
5
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6
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1.1k
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 12 months ago by ★ 4.8k • written 12 months ago by ▴ 70
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3
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672
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 12 months ago by 68k • written 12 months ago by • 0
0
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2
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703
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 12 months ago by 68k • written 12 months ago by • 0
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2
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650
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
13 months ago Chanderkant Chaudhary • 0
8
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5
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2.5k
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 5 months ago by 52k • written 13 months ago by ▴ 60
0
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2
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680
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 13 months ago by 52k • written 13 months ago by • 0
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2
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936
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 13 months ago by 43k • written 13 months ago by • 0
1
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3
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849
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 14 months ago by • 0
0
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4
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816
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
14 months ago • updated 13 months ago mperalc • 0
0
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0
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626
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
14 months ago Abril • 0
2
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1
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617
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 14 months ago by ★ 4.8k • written 14 months ago by • 0
3
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2
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722
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
14 months ago Shaimaa Gamal • 0
4
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3
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903
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 14 months ago by 52k • written 14 months ago by • 0
2
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3
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838
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 14 months ago by 68k • written 14 months ago by • 0
2
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1
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558
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 14 months ago by 43k • written 14 months ago by ▴ 20
0
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2
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644
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PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 14 months ago by 43k • written 14 months ago by • 0
5
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6
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1.2k
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
15 months ago Shaimaa Gamal • 0
4
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6
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1.3k
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 14 months ago by 52k • written 15 months ago by • 0
3
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1
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686
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Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 15 months ago by 52k • written 15 months ago by • 0
50 results • Page 1 of 1
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Answer: EuroBioC2024 abstract submission is open! by Ali • 0
[Promo products][1] are a smart way to boost visibility, especially with exciting updates like *News: EuroBioC2024 abstract submission is o…
Answer: ROAST for small sets by Gordon Smyth 52k
The p-values from `mroast` will be the same (up to sampling variability associated with random rotations) regardless of whether you test al…
Comment: FlowSOM library requires igraph but igraph does not install by Szabolcs • 0
The R/igraph Installation FAQ covers most issues: https://r.igraph.org/articles/installation-troubleshooting.html
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much for the vis suggestion!
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much - I appreciate the mathematical explanation and link to Dr. Phipson's thesis!
Votes
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
Comment: edgeR::cpm() results in negative values from raw counts of 0
Comment: edgeR::cpm() results in negative values from raw counts of 0
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