Showing : DifferentialExpression • reset
3
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6
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502
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 14 days ago by • 0
2
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2
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241
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Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
16 days ago • updated 15 days ago jamie.gearing ▴ 60
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4
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185
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
20 days ago • updated 17 days ago Denise • 0
0
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1
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573
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Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 6 months ago by 43k • written 6 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 7 months ago by ★ 5.0k • written 7 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
0
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3
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995
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Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 9 months ago by 43k • written 9 months ago by • 0
0
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1
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404
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 9 months ago by 43k • written 10 months ago by • 0
0
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1
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644
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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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718
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Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 10 months ago by • 0
0
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2
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712
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
11 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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933
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 12 months ago by 53k • written 12 months ago by • 0
1
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3
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872
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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
528
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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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971
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 15 months ago by 53k • written 15 months ago by • 0
3
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3
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1.6k
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the count matrix have decimal values
DESeq2 DifferentialExpression
updated 15 months ago by 68k • written 15 months ago by • 0
0
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3
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1.0k
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comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 15 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 15 months ago by ★ 1.4k • written 16 months ago by • 0
0
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3
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996
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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 16 months ago by ★ 5.0k • written 16 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 16 months ago by 68k • written 16 months ago by • 0
0
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0
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799
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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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3.3k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 17 months ago by • 0 • written 21 months ago by ▴ 60
2
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1
reply
821
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DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by ▴ 70
0
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4
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1.3k
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
18 months ago • updated 17 months ago vohara4 • 0
0
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1
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643
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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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787
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Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 18 months ago by 43k • written 18 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 18 months ago by 53k • written 18 months ago by • 0
0
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1
reply
628
views
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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1.4k
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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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914
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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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824
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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
vote
3
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914
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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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1.0k
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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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885
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DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
20 months ago Chanderkant Chaudhary • 0
8
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5
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3.3k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 13 months ago by 53k • written 20 months ago by ▴ 60
0
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2
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873
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 20 months ago by 53k • written 20 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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1.0k
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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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1.0k
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Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
21 months ago mperalc • 0
0
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0
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764
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Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
21 months ago Abril • 0
2
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1
reply
800
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Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 21 months ago by ★ 5.0k • written 21 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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1.1k
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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
reply
759
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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
Recent ...
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Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Votes
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
Comment: upstream git branches of bioc-release
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