Showing : differentialexpression • reset
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Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 3 months ago by 43k • written 4 months ago by • 0
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1
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1.2k
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Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 5 months ago by ★ 4.9k • written 5 months ago by • 0
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8
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2.8k
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
5 months ago ktz • 0
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3
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839
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 6 months ago by 43k • written 7 months ago by • 0
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1
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333
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 7 months ago by 43k • written 7 months ago by • 0
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1
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462
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 7 months ago by 43k • written 7 months ago by • 0
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5
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616
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 7 months ago by • 0
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2
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620
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
9 months ago Tadeoye ▴ 20
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9
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1.5k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 9 months ago by 68k • written 9 months ago by • 0
3
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3
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852
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 10 months ago by 53k • written 10 months ago by • 0
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3
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778
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
10 months ago • updated 9 months ago abadgerw • 0
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5
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1.1k
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
10 months ago • updated 9 months ago abadgerw • 0
0
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1
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466
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
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6
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1.3k
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[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 10 months ago by 43k • written 11 months ago by • 0
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3
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859
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 13 months ago by 53k • written 13 months ago by • 0
3
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3
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1.5k
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 13 months ago by 68k • written 13 months ago by • 0
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3
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946
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 13 months ago by • 0
3
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5
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2.2k
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DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 13 months ago by ★ 1.4k • written 13 months ago by • 0
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3
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900
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 14 months ago by ★ 4.9k • written 14 months ago by • 0
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5
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1.0k
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Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 14 months ago by 68k • written 14 months ago by • 0
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0
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746
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
14 months ago nhaus ▴ 70
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5
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3.1k
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 15 months ago by • 0 • written 18 months ago by ▴ 60
2
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1
reply
753
views
DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 15 months ago by 68k • written 15 months ago by ▴ 70
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4
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1.1k
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
15 months ago vohara4 • 0
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1
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597
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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 15 months ago by 68k • written 15 months ago by • 0
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3
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718
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 16 months ago by 43k • written 16 months ago by • 0
1
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3
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1.0k
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 16 months ago by 53k • written 16 months ago by • 0
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1
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578
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 16 months ago by ★ 4.9k • written 16 months ago by • 0
2
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7
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1.8k
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
16 months ago sajadahmad41454 • 0
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3
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1.4k
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Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 16 months ago by ★ 4.9k • written 16 months ago by • 0
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3
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833
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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 16 months ago by 68k • written 16 months ago by • 0
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2
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759
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 17 months ago by 43k • written 17 months ago by ▴ 70
5
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6
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1.4k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 17 months ago by ★ 4.9k • written 17 months ago by ▴ 70
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3
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806
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by • 0
0
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2
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924
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What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by • 0
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2
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808
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
18 months ago Chanderkant Chaudhary • 0
8
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5
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3.1k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 10 months ago by 53k • written 18 months ago by ▴ 60
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2
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799
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 18 months ago by 53k • written 18 months ago by • 0
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2
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1.1k
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Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 18 months ago by 43k • written 18 months ago by • 0
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3
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956
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 19 months ago by • 0
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4
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953
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
18 months ago mperalc • 0
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0
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722
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
19 months ago Abril • 0
2
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1
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734
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 19 months ago by ★ 4.9k • written 19 months ago by • 0
3
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2
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867
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
19 months ago Shaimaa Gamal • 0
4
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3
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1.0k
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voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 19 months ago by 53k • written 19 months ago by • 0
2
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3
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1.0k
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 19 months ago by 68k • written 19 months ago by • 0
2
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1
reply
680
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 19 months ago by 43k • written 19 months ago by ▴ 20
0
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2
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769
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PCA after DESeq2
DESeq2 PrincipalComponent prin DifferentialExpression
updated 19 months ago by 43k • written 19 months ago by • 0
5
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6
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1.4k
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Monotonic genes in results of differential gene expression analysis
DifferentialExpression rnaseqGene RNASeqData
20 months ago Shaimaa Gamal • 0
4
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6
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1.5k
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filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 19 months ago by 53k • written 20 months ago by • 0
198 results • Page 1 of 4
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Comment: GO.db and others package Download failure by James W. MacDonald 68k
Also, you never need to use anything but `BiocManager::install` to install any package, which has the beneficial side effect of ensuring th…
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Yes. Your packages have odd Y version numbers (where the version is X.Y.Z). That means they are devel packages (release versions have even …
Comment: GO.db and others package Download failure by Skyler • 0
Am I using Bioc-devel?
Comment: GO.db and others package Download failure by James W. MacDonald 68k
Is there a reason to use Bioc-devel? If not, you should be using the release version (which I am, and which installs `GO.db` without compla…
Comment: GO.db and others package Download failure by Skyler • 0
Hi James, Below I have inserted all of my code. I have run r as an administrator and not as an administrator. I have changed my CRANmirror …
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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