Showing : differentialexpression • reset
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Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
3 days ago • updated 2 days ago Ahmed Salah • 0
2
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2
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201
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Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
6 days ago • updated 5 days ago jamie.gearing ▴ 60
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4
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153
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Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
9 days ago • updated 6 days ago Denise • 0
0
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1
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568
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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
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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
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DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
7 months ago ktz • 0
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3
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982
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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
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1
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397
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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 9 months ago by • 0
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1
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636
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DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 9 months ago by 43k • written 9 months ago by • 0
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5
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704
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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
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2
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703
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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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1.7k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 11 months ago by 68k • written 11 months ago by • 0
3
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3
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917
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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
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864
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
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
12 months ago • updated 11 months ago abadgerw • 0
0
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1
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525
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How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 13 months ago by 43k • written 13 months ago by • 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 13 months ago by • 0
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3
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958
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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
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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
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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 15 months ago by • 0
0
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3
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986
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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
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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
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0
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794
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Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
16 months ago nhaus ▴ 70
3
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5
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3.3k
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Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 17 months ago by • 0 • written 20 months ago by ▴ 60
2
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1
reply
813
views
DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by ▴ 70
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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
17 months ago vohara4 • 0
0
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1
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641
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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 17 months ago by 68k • written 17 months ago by • 0
0
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3
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782
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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
views
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
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626
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Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
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7
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1.9k
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deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
18 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 19 months ago by ★ 5.0k • written 19 months ago by • 0
0
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3
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907
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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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820
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Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 19 months ago by 43k • written 19 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 19 months ago by ★ 5.0k • written 19 months ago by ▴ 70
1
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3
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906
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 19 months ago by 68k • written 19 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 19 months ago by 68k • written 19 months ago by • 0
1
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2
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878
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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
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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 20 months ago by ▴ 60
0
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2
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868
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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 20 months ago by 43k • written 20 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
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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
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0
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763
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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
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793
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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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1.0k
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Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
21 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 21 months ago by 53k • written 21 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 21 months ago by 68k • written 21 months ago by • 0
2
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1
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752
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Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 21 months ago by 43k • written 22 months ago by ▴ 20
201 results • Page 1 of 5
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Comment: gene Set with high AUC score but no cells assigned to cell type by gogeni5529 • 0
THIS is spam. How Do I delete it?
Comment: limpa - drivers for unusually high standard error? by Julia Broadbent • 0
Apologies for not being clearer in my initial question, but thank you for answering regardless! The large SE values I am looking at appear …
Answer: limpa - drivers for unusually high standard error? by Gordon Smyth 53k
Hi Julia, I am going to assume that you mean standard errors (SEs) returned by `dpcQuant()`, because later stages in the limpa pipeline do…
Comment: gene Set with high AUC score but no cells assigned to cell type by e.j.aaw.g.erm • 0
It sounds like AUCell is struggling with thresholding because your cDC2 gene set doesn t show a clear bimodal distribution. While a high AU…
Comment: featureCounts -L: high unassigned:mapq fraction by insurancetaaddddaxrealty • 0
FeatureCounts can behave differently with ONT cDNA BAM files due to long read splice patterns, and many users compare settings or presets m…
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Answer: gene Set with high AUC score but no cells assigned to cell type
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
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