Showing : DifferentialExpression • reset
3
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 29 days ago by • 0
2
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2
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271
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Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
4 weeks ago jamie.gearing ▴ 60
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4
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214
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
5 weeks ago • updated 4 weeks ago Denise • 0
0
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1
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598
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Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 6 months ago by 43k • written 7 months ago by • 0
1
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1
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1.3k
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Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
1
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8
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3.0k
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
8 months ago ktz • 0
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3
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1.0k
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 10 months ago by 43k • written 10 months ago by • 0
0
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1
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420
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 10 months ago by 43k • written 10 months ago by • 0
0
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1
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670
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 10 months ago by 43k • written 10 months ago by • 0
0
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5
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742
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 11 months ago by • 0
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2
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731
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
12 months ago Tadeoye ▴ 20
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9
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1.8k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 12 months ago by 68k • written 12 months ago by • 0
3
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3
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959
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 13 months ago by 53k • written 13 months ago by • 0
1
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3
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897
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
13 months ago • updated 12 months ago abadgerw • 0
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5
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1.2k
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
13 months ago • updated 12 months ago abadgerw • 0
0
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1
reply
545
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 14 months ago by 43k • written 14 months ago by • 0
0
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6
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1.4k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 13 months ago by 43k • written 14 months ago by • 0
0
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3
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994
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 16 months ago by 53k • written 16 months ago by • 0
3
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3
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1.7k
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 16 months ago by 68k • written 16 months ago by • 0
0
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3
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1.1k
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 16 months ago by • 0
3
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5
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2.3k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 16 months ago by ★ 1.4k • written 16 months ago by • 0
0
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3
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1.0k
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 17 months ago by ★ 5.0k • written 17 months ago by • 0
2
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5
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1.1k
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by • 0
0
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0
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821
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
17 months ago nhaus ▴ 70
3
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5
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3.4k
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 18 months ago by • 0 • written 21 months ago by ▴ 60
2
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1
reply
842
views
DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 18 months ago by 68k • written 18 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
18 months ago vohara4 • 0
0
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1
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653
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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 18 months ago by 68k • written 18 months ago by • 0
0
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3
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803
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 19 months ago by 43k • written 19 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 19 months ago by 53k • written 19 months ago by • 0
0
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1
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640
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
2
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7
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2.0k
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
19 months ago sajadahmad41454 • 0
0
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3
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1.5k
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
0
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3
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939
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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 19 months ago by 68k • written 19 months ago by • 0
0
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2
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837
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 20 months ago by 43k • written 20 months ago by ▴ 70
5
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6
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1.5k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 20 months ago by ★ 5.0k • written 20 months ago by ▴ 70
1
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3
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938
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 20 months ago by 68k • written 20 months ago by • 0
0
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2
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1.1k
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 20 months ago by 68k • written 20 months ago by • 0
1
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2
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899
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
21 months ago Chanderkant Chaudhary • 0
8
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5
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3.4k
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What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 13 months ago by 53k • written 21 months ago by ▴ 60
0
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2
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894
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 21 months ago by 53k • written 21 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 21 months ago by 43k • written 21 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 22 months ago by • 0
0
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4
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1.1k
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
22 months ago • updated 21 months ago mperalc • 0
0
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0
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774
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
22 months ago Abril • 0
2
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1
reply
811
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 22 months ago by ★ 5.0k • written 22 months ago by • 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
22 months ago Shaimaa Gamal • 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 22 months ago by 53k • written 22 months ago by • 0
2
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3
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1.2k
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 22 months ago by 68k • written 22 months ago by • 0
2
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1
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775
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 22 months ago by 43k • written 22 months ago by ▴ 20
201 results • Page 1 of 5
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Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in by jtsy6383 • 0
Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in by Gordon Smyth 53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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