Showing : DifferentialExpression • reset
3
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1.0k
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 8 weeks ago by • 0
2
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2
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313
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Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
8 weeks ago jamie.gearing ▴ 60
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4
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275
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
9 weeks ago • updated 8 weeks ago Denise • 0
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1
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2.5k
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How to interpret MAST coefficients
DifferentialExpression MAST
updated 7 months ago by ▴ 10 • written 3.3 years ago by • 0
0
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1
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629
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Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 7 months ago by 43k • written 8 months ago by • 0
1
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1
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1.4k
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Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
1
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8
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3.1k
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
9 months ago ktz • 0
0
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3
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1.1k
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 11 months ago by 43k • written 11 months ago by • 0
0
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1
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469
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 11 months ago by 43k • written 11 months ago by • 0
0
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5
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796
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 12 months ago by • 0
0
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1
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719
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
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2
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782
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
13 months ago Tadeoye ▴ 20
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9
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1.9k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 13 months ago by 68k • written 13 months ago by • 0
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5
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1.3k
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
14 months ago • updated 13 months ago abadgerw • 0
1
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3
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962
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
14 months ago • updated 13 months ago abadgerw • 0
3
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3
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1000
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 14 months ago by 53k • written 14 months ago by • 0
8
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5
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 14 months ago by 53k • written 22 months ago by ▴ 60
0
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6
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1.5k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 14 months ago by 43k • written 15 months ago by • 0
0
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1
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564
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
0
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3
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1.2k
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 17 months ago by • 0
0
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3
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1.0k
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 17 months ago by 53k • written 17 months ago by • 0
3
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3
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1.8k
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by • 0
3
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5
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2.5k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
0
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3
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1.0k
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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 18 months ago by ★ 5.0k • written 18 months ago by • 0
2
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5
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1.2k
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 18 months ago by 68k • written 18 months ago by • 0
0
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0
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859
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
18 months ago nhaus ▴ 70
3
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5
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3.7k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 19 months ago by • 0 • written 22 months ago by ▴ 60
2
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1
reply
881
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 19 months ago by 68k • written 19 months ago by ▴ 70
0
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4
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1.3k
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
19 months ago vohara4 • 0
0
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1
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692
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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 19 months ago by 68k • written 19 months ago by • 0
0
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3
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835
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 20 months ago by 43k • written 20 months ago by • 0
1
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3
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1.1k
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 20 months ago by 53k • written 20 months ago by • 0
2
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7
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2.1k
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
20 months ago sajadahmad41454 • 0
0
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1
reply
656
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
0
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3
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1.6k
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
0
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3
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999
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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 20 months ago by 68k • written 20 months ago by • 0
5
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6
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1.6k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 21 months ago by ★ 5.0k • written 21 months ago by ▴ 70
0
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2
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907
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 21 months ago by 43k • written 21 months ago by ▴ 70
1
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3
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968
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 21 months ago by 68k • written 21 months ago by • 0
0
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2
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1.1k
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 21 months ago by 68k • written 21 months ago by • 0
1
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2
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926
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
22 months ago Chanderkant Chaudhary • 0
0
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2
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916
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 22 months ago by 53k • written 22 months ago by • 0
0
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2
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1.2k
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 22 months ago by 43k • written 22 months ago by • 0
1
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3
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1.1k
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 23 months ago by • 0
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4
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1.1k
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
23 months ago • updated 22 months ago mperalc • 0
2
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1
reply
837
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
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0
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799
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
23 months ago Abril • 0
3
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2
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1.1k
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
23 months ago Shaimaa Gamal • 0
4
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6
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1.8k
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 23 months ago by 53k • written 2.0 years ago by • 0
4
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3
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1.2k
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 23 months ago by 53k • written 23 months ago by • 0
201 results • Page 1 of 5
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Comment: Pairwise comparison of multiple groups with different base by ja569116 • 0
Hi @mikelove I have a similar situation, and I feel that I have interpreted the results in the wrong way. In my case I would like to identi…
Comment: Are individual-mouse-based statistics possible in CellChat? by TikTsossakaas33ocissalpc • 0
Questions about comparing groups and statistical significance highlight how data driven thinking matters across fields. In online mobile ga…
Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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