Showing : differentialexpression • reset
3
votes
6
replies
1.0k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 8 weeks ago by • 0
2
votes
2
replies
313
views
Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
8 weeks ago jamie.gearing ▴ 60
0
votes
4
replies
276
views
Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
9 weeks ago • updated 8 weeks ago Denise • 0
0
votes
1
reply
629
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 7 months ago by 43k • written 8 months ago by • 0
1
vote
1
reply
1.4k
views
Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
1
vote
8
replies
3.1k
views
DESeq: Gene is not flagged as differentially expressed despite count data showing differences
DifferentialExpression DESeq2
9 months ago ktz • 0
0
votes
3
replies
1.1k
views
Differential variance analysis - can i use deseq2
DESeq2 DifferentialExpression RNASeq RNASeqData scRNAseq
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
1
reply
469
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
1
reply
720
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 11 months ago by 43k • written 11 months ago by • 0
0
votes
5
replies
797
views
Is there a way to do DEG analysis across two batches sharing one sample only?
DESeq2 DifferentialExpression RNASeqData BatchEffect
written 12 months ago by • 0
0
votes
2
replies
782
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
13 months ago Tadeoye ▴ 20
0
votes
9
replies
1.9k
views
Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 13 months ago by 68k • written 13 months ago by • 0
3
votes
3
replies
1.0k
views
Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 14 months ago by 53k • written 14 months ago by • 0
1
vote
3
replies
962
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
14 months ago • updated 13 months ago abadgerw • 0
0
votes
5
replies
1.3k
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
14 months ago • updated 13 months ago abadgerw • 0
0
votes
1
reply
564
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 15 months ago by 43k • written 15 months ago by • 0
0
votes
6
replies
1.5k
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 14 months ago by 43k • written 15 months ago by • 0
0
votes
3
replies
1.0k
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 17 months ago by 53k • written 17 months ago by • 0
3
votes
3
replies
1.8k
views
the count matrix have decimal values
DESeq2 DifferentialExpression
updated 17 months ago by 68k • written 17 months ago by • 0
0
votes
3
replies
1.2k
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 17 months ago by • 0
3
votes
5
replies
2.5k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 17 months ago by ★ 1.4k • written 17 months ago by • 0
0
votes
3
replies
1.0k
views
Error when trying to do different pairwise comparisons and lfcshrink than what's listed on resultsNames()
RNASeqData DESeq2 RNASeq DifferentialExpression
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
2
votes
5
replies
1.2k
views
Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 18 months ago by 68k • written 18 months ago by • 0
0
votes
0
replies
859
views
Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
18 months ago nhaus ▴ 70
3
votes
5
replies
3.7k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 19 months ago by • 0 • written 22 months ago by ▴ 60
2
votes
1
reply
881
views
DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 19 months ago by 68k • written 19 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
19 months ago vohara4 • 0
0
votes
1
reply
692
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
3
replies
836
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 20 months ago by 43k • written 20 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 20 months ago by 53k • written 20 months ago by • 0
0
votes
1
reply
656
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
2
votes
7
replies
2.1k
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
20 months ago sajadahmad41454 • 0
0
votes
3
replies
1.6k
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 20 months ago by ★ 5.0k • written 20 months ago by • 0
0
votes
3
replies
999
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 20 months ago by 68k • written 20 months ago by • 0
0
votes
2
replies
908
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 21 months ago by 43k • written 21 months ago by ▴ 70
5
votes
6
replies
1.6k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 21 months ago by ★ 5.0k • written 21 months ago by ▴ 70
1
vote
3
replies
968
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 21 months ago by 68k • written 21 months ago by • 0
0
votes
2
replies
1.1k
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 21 months ago by 68k • written 21 months ago by • 0
1
vote
2
replies
926
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
22 months ago Chanderkant Chaudhary • 0
8
votes
5
replies
3.6k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 14 months ago by 53k • written 22 months ago by ▴ 60
0
votes
2
replies
916
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 22 months ago by 53k • written 22 months ago by • 0
0
votes
2
replies
1.2k
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 22 months ago by 43k • written 22 months ago by • 0
1
vote
3
replies
1.1k
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 23 months ago by • 0
0
votes
4
replies
1.1k
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
23 months ago mperalc • 0
0
votes
0
replies
800
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
23 months ago Abril • 0
2
votes
1
reply
837
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 23 months ago by ★ 5.0k • written 23 months ago by • 0
3
votes
2
replies
1.1k
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
23 months ago Shaimaa Gamal • 0
4
votes
3
replies
1.2k
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 23 months ago by 53k • written 23 months ago by • 0
2
votes
3
replies
1.2k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 23 months ago by 68k • written 23 months ago by • 0
2
votes
1
reply
802
views
Continuous variable to identify responder genes using DESeq2
DESeq2 rnaseqGene DifferentialExpression
updated 23 months ago by 43k • written 23 months ago by ▴ 20
201 results • Page 1 of 5
Recent ...
Replies
Comment: limpa analysis advice by Gordon Smyth 53k
Yes, we use Astral currently. The main dataset in the limpa preprint is Astral. I don't see any major problems with your data and I think …
Comment: limpa analysis advice by SamGG ▴ 360
Thank you for your comments. Please note that I did not apply any filtering to the peptide intensity. The experimental protocol includes tw…
Comment: Pairwise comparison of multiple groups with different base by ja569116 • 0
Hi @mikelove I have a similar situation, and I feel that I have interpreted the results in the wrong way. In my case I would like to identi…
Comment: Are individual-mouse-based statistics possible in CellChat? by TikTsossakaas33ocissalpc • 0
Questions about comparing groups and statistical significance highlight how data driven thinking matters across fields. In online mobile ga…
Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Votes
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Awards • All
Popular Question to A • 0
Popular Question to Lluís Revilla Sancho ▴ 760
Popular Question to nromerov • 0
Popular Question to Thomas Girke ★ 1.7k
Teacher to Gordon Smyth 53k
Locations • All
Barcelona, Spain, 5 minutes ago
Germany, 5 minutes ago
Austria, 17 minutes ago
Wageningen University, Wageningen, the Netherlands, 22 minutes ago
The city by the bay, 30 minutes ago
Traffic: 1469 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