Showing : differentialexpression • reset
2
votes
3
replies
114
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
2 days ago • updated 1 day ago Ahmed Salah • 0
2
votes
2
replies
182
views
Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
4 days ago jamie.gearing ▴ 60
0
votes
4
replies
145
views
Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
8 days ago • updated 5 days ago Denise • 0
0
votes
1
reply
566
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 5 months ago by 43k • written 6 months ago by • 0
1
vote
1
reply
1.3k
views
Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
1
vote
8
replies
3.0k
views
DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
7 months ago ktz • 0
0
votes
3
replies
982
views
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
votes
1
reply
397
views
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
0
votes
1
reply
636
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 9 months ago by 43k • written 9 months ago by • 0
0
votes
5
replies
702
views
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
votes
2
replies
703
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
11 months ago Tadeoye ▴ 20
0
votes
9
replies
1.7k
views
Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 11 months ago by 68k • written 11 months ago by • 0
3
votes
3
replies
913
views
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
vote
3
replies
862
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
12 months ago abadgerw • 0
0
votes
5
replies
1.2k
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
12 months ago • updated 11 months ago abadgerw • 0
0
votes
1
reply
525
views
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
0
votes
6
replies
1.4k
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 13 months ago by 43k • written 13 months ago by • 0
0
votes
3
replies
958
views
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
votes
3
replies
1.6k
views
the count matrix have decimal values
DESeq2 DifferentialExpression
updated 15 months ago by 68k • written 15 months ago by • 0
0
votes
3
replies
1.0k
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 15 months ago by • 0
3
votes
5
replies
2.3k
views
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
votes
3
replies
985
views
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
votes
5
replies
1.1k
views
Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 16 months ago by 68k • written 16 months ago by • 0
0
votes
0
replies
794
views
Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
16 months ago nhaus ▴ 70
3
votes
5
replies
3.3k
views
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
votes
1
reply
812
views
DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by ▴ 70
0
votes
4
replies
1.3k
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
17 months ago vohara4 • 0
0
votes
1
reply
640
views
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
votes
3
replies
782
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 18 months ago by 43k • written 18 months ago by • 0
1
vote
3
replies
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
votes
1
reply
624
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
2
votes
7
replies
1.9k
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
18 months ago sajadahmad41454 • 0
0
votes
3
replies
1.4k
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 18 months ago by ★ 5.0k • written 19 months ago by • 0
0
votes
3
replies
905
views
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
votes
2
replies
817
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 19 months ago by 43k • written 19 months ago by ▴ 70
5
votes
6
replies
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
vote
3
replies
906
views
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
votes
2
replies
1.0k
views
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
vote
2
replies
876
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
20 months ago Chanderkant Chaudhary • 0
8
votes
5
replies
3.3k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 12 months ago by 53k • written 20 months ago by ▴ 60
0
votes
2
replies
867
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 20 months ago by 53k • written 20 months ago by • 0
0
votes
2
replies
1.2k
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 20 months ago by 43k • written 20 months ago by • 0
1
vote
3
replies
1.0k
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 22 months ago by • 0
0
votes
4
replies
1.0k
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
21 months ago mperalc • 0
0
votes
0
replies
763
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
21 months ago Abril • 0
2
votes
1
reply
792
views
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
votes
2
replies
1.0k
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
21 months ago Shaimaa Gamal • 0
4
votes
3
replies
1.2k
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 21 months ago by 53k • written 21 months ago by • 0
2
votes
3
replies
1.1k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 21 months ago by 68k • written 21 months ago by • 0
2
votes
1
reply
752
views
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
Recent ...
Replies
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…
Comment: A problem occurs when running the monocle2 by e.j.aaw.g.erm • 0
For gamers facing technical issues or errors in complex scripts, the Redz Hub script download provides a reliable tool to optimize performa…
Answer: How can I correctly use phyloseq with Docker? by Kevin Blighe ★ 4.0k
The Bioconductor version must be compatible with the R version. Bioconductor version 3.18 is compatible with R version 4.3. The Dockerfile …
Answer: Boolean Gate Combination for Any 2 Positive Events in flowWorkspace by Kevin Blighe ★ 4.0k
Your proposed code is correct and will achieve the desired outcome. The boolean filter expression `IFNg & TNFa | IFNg & IL2 | TNFa & IL2` i…
Answer: Guidance Requested on GCN Network Analysis and Module Enrichment in R by Kevin Blighe ★ 4.0k
The discrepancy between `final_exp1` and `final_exp2` could arise from several factors, despite matching dimensions. The `identical()` func…
Votes
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?
Answer: Identifying differentially expressed genes in individual samples from a large co
Awards • All
Popular Question to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Supporter to fabio.marroni • 0
Popular Question to Guido Hooiveld ★ 4.1k
Popular Question to James W. MacDonald 68k
Locations • All
The city by the bay, 2 hours ago
WEHI, Melbourne, Australia, 7 hours ago
Australia/Melbourne/Monash University Genomics and Bioinformatics Platform, 8 hours ago
Pakistan, 9 hours ago
Pakistan, 10 hours ago
Traffic: 647 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6