Showing : differentialexpression • reset
0
votes
5
replies
270
views
Lowly expressed genes reported as significant when using lfcThreshold in DESeq
RNASeq DESeq2 DifferentialExpression
updated 16 days ago by 43k • written 16 days ago by • 0
3
votes
6
replies
1.1k
views
Highly similar RNA-seq samples in PCA - pooling or technical duplication?
RNASeq DESeq2 DifferentialExpression RNASeqData
written 12 weeks ago by • 0
2
votes
2
replies
347
views
Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
12 weeks ago jamie.gearing ▴ 60
0
votes
4
replies
347
views
Getting a large intercept with DESeq2
DESeq2 DifferentialExpression TimeCourse
3 months ago • updated 12 weeks ago Denise • 0
0
votes
1
reply
672
views
Difference in DESeq2 output and tidybulk DESeq2 method
DifferentialExpression DESeq2 tidybulk RNASeq
updated 8 months ago by 43k • written 9 months ago by • 0
1
vote
1
reply
1.4k
views
Differential expression analysis using two TCGA datasets
DifferentialExpression TCGAbiolinks RNASeq
updated 10 months ago by ★ 5.0k • written 10 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
10 months ago ktz • 0
0
votes
3
replies
1.2k
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
508
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 12 months ago by 43k • written 12 months ago by • 0
0
votes
1
reply
770
views
DEG analysis across multiple timepoints, treatments and tissues
DifferentialExpression RNASeq DESeq2
updated 12 months ago by 43k • written 12 months ago by • 0
0
votes
5
replies
828
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
812
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
14 months ago Tadeoye ▴ 20
0
votes
9
replies
2.0k
views
Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 14 months ago by 68k • written 14 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 15 months ago by • 0
1
vote
3
replies
1.0k
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
15 months ago • updated 14 months ago abadgerw • 0
0
votes
5
replies
1.3k
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
15 months ago • updated 14 months ago abadgerw • 0
0
votes
1
reply
598
views
How to set filtering standard for low-expression genes in ImpulseDE2
DifferentialExpression ImpulseDE2 DESeq2
updated 16 months ago by 43k • written 16 months ago by • 0
0
votes
6
replies
1.5k
views
[DESeq2] Introduce a bias in DESeq2
DifferentialExpression DESeq2 BatchEffect
updated 15 months ago by 43k • written 16 months ago by • 0
0
votes
3
replies
1.1k
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 18 months ago by 53k • written 18 months ago by • 0
3
votes
3
replies
1.9k
views
the count matrix have decimal values
DESeq2 DifferentialExpression
updated 18 months ago by 68k • written 18 months ago by • 0
0
votes
3
replies
1.3k
views
comparing common differentially expressed genes from two Rna-Seq Dataset.
DESeq2 edgeR DifferentialExpression
written 18 months ago by • 0
3
votes
5
replies
2.8k
views
DESeq2: How to Compare the Condition Effects of Two Different Treatments?
DESeq2 RNAseq DifferentialExpression
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
0
votes
3
replies
1.1k
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 19 months ago by • 0
0
votes
0
replies
929
views
Linear Mixed Model for Differential Gene Expression in Single-Cell RNAseq with Batch Effects
lmer MAST DifferentialExpression
19 months ago nhaus ▴ 70
3
votes
5
replies
4.2k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 20 months ago by • 0 • written 23 months ago by ▴ 60
2
votes
1
reply
947
views
DESeq2 returns results for group with just one replicate
DESeq2 DifferentialExpression
updated 20 months ago by 68k • written 20 months ago by ▴ 70
0
votes
4
replies
1.4k
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
20 months ago vohara4 • 0
0
votes
1
reply
719
views
How to identify transcripts/genes with differential kinetics in two genotypes, using time-course RNA seq data?
RNASeqData DESeq2 DifferentialExpression
updated 20 months ago by 68k • written 20 months ago by • 0
0
votes
3
replies
863
views
Assymetric MA plot with no overall trend
DESeq2 DifferentialExpression
updated 21 months ago by 43k • written 21 months ago by • 0
1
vote
3
replies
1.2k
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 21 months ago by 53k • written 21 months ago by • 0
0
votes
1
reply
671
views
Differential gene expression analysis results
DESeq2 DifferentialExpression
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
2
votes
7
replies
2.1k
views
deseq2 results
DESeq2 DifferentialExpression rnaseqGene DifferentialRegulation
21 months ago sajadahmad41454 • 0
0
votes
3
replies
1.8k
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 21 months ago by ★ 5.0k • written 21 months ago by • 0
0
votes
3
replies
1.1k
views
Assist me in determining whether the analysis process using the limma package has been executed correctly.
GEOquery ArrayExpress limma DifferentialExpression
updated 21 months ago by 68k • written 21 months ago by • 0
0
votes
2
replies
944
views
Interaction term vs grouping variable design considerations
DESeq2 DifferentialExpression
updated 22 months ago by 43k • written 22 months ago by ▴ 70
5
votes
6
replies
1.7k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 22 months ago by ★ 5.0k • written 22 months ago by ▴ 70
1
vote
3
replies
989
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 22 months ago by 68k • written 22 months ago by • 0
0
votes
2
replies
1.2k
views
What to the log 2 fold changes mean using LRT on time course in DESeq2
DESeq2 timecourse DifferentialExpression
updated 22 months ago by 68k • written 22 months ago by • 0
1
vote
2
replies
959
views
DESeq2 "Contrast" option
DESeq2 contrast DifferentialExpression
23 months ago • updated 22 months ago Chanderkant Chaudhary • 0
8
votes
5
replies
3.9k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 15 months ago by 53k • written 23 months ago by ▴ 60
0
votes
2
replies
936
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 23 months ago by 53k • written 23 months ago by • 0
0
votes
2
replies
1.3k
views
Missing Band on Volcano Plot from DESeq2
DESeq2 Visualization DifferentialExpression
updated 23 months ago by 43k • written 23 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 2.0 years 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
834
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
24 months ago Abril • 0
2
votes
1
reply
860
views
Normalization factors when there is a possible unidirectional expression
limma Normalization DifferentialExpression
updated 24 months ago by ★ 5.0k • written 24 months ago by • 0
3
votes
2
replies
1.2k
views
Design matrix after RUVg correction
RUVSeq limma DifferentialExpression
2.0 years ago Shaimaa Gamal • 0
4
votes
3
replies
1.3k
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 2.0 years ago by 53k • written 2.0 years ago by • 0
2
votes
3
replies
1.2k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 2.0 years ago by 68k • written 2.0 years ago by • 0
202 results • Page 1 of 5
Recent ...
Replies
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2 by colinmccornack • 0
FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Erik Wright ▴ 160
This has to do with the fact that some taxonomies reuse names at the same rank level. Common examples in the SILVA taxonomy are "Incertae S…
Comment: Deseq2 DE analysis of host-pathogen samples (model separately or jointly?) by a2a2ddrhaa • 0
For those taking a break from the lab, the CT777 Game download https://ct7777.pk/ offers a high-performance entry into online mobile gaming…
Votes
A: WGCNA sample size minimum: why?
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
Answer: Can you colour dendrogram branch clusters in pheatmap?
Comment: Are transformed values from rlog /vst log2 normalized counts?
Are transformed values from rlog /vst log2 normalized counts?
Awards • All
Popular Question to Peter Hickey ▴ 760
Popular Question to Sean Davis 21k
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.3k
Popular Question to Andreas Zankl ▴ 80
Locations • All
Austria, 3 minutes ago
United States, 35 minutes ago
United States, 41 minutes ago
United States, 42 minutes ago
Germany, 49 minutes ago
Traffic: 1348 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