Showing : differential gene expression • reset
17
votes
14
replies
54k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 3.6 years ago by • 0 • written 8.5 years ago by ▴ 20
4
votes
6
replies
29k
views
Design model for DESeq2 analysis
deseq2 differential gene expression
updated 8.2 years ago by ▴ 690 • written 8.2 years ago by ▴ 20
3
votes
12
replies
28k
views
P Value of 0?
differential gene expression edger
updated 10.9 years ago by ▴ 180 • written 10.9 years ago by • 0
6
votes
12
replies
20k
views
Problem making DESeq dataset; Error all variables in design formula must be columns in colData
deseq2 deseq counts rnaseq differential gene expression
updated 9.7 years ago by 43k • written 9.7 years ago by ▴ 10
18
votes
37
replies
19k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma illumina differential gene expression multiple comparisons design matrix
10.6 years ago • updated 10.5 years ago svlachavas ▴ 840
10
votes
14
replies
15k
views
how DESeq calculates p-value ?
deseq differential gene expression statistics p-value
updated 4.9 years ago by ▴ 20 • written 9.9 years ago by ▴ 30
11
votes
8
replies
13k
views
Limma and batch effect
limma differential gene expression clustering removebatcheffect
updated 8.4 years ago by 53k • written 8.4 years ago by ▴ 80
3
votes
3
replies
10k
views
TPM data Differential expression analysis
edger limma differential gene expression
updated 3.7 years ago by 53k • written 7.7 years ago by • 0
3
votes
5
replies
10k
views
How to find Top 10 expressed genes in DESeq2
deseq2 baseMean differential gene expression rnaseqgene
updated 7.0 years ago by ★ 1.4k • written 7.0 years ago by • 0
5
votes
12
replies
10k
views
Filtering step for differential analysis in edgeR
r edger differential gene expression filtering bioconductor
updated 7.7 years ago by 53k • written 7.7 years ago by ▴ 120
2
votes
2
replies
9.5k
views
edgeR: How is FDR calculated for logFC? (False Discovery Rate)
edgeR bioconductor fdr statistics differential gene expression
9.1 years ago jol.espinoz ▴ 40
5
votes
14
replies
7.7k
views
Possible ways to select differential expressed genes using DeSeq2 or edgeR
R deseq2 edger differential gene expression fold change
updated 3.7 years ago by ★ 5.0k • written 7.5 years ago by ▴ 60
7
votes
6
replies
7.5k
views
scaling data for clustering heat map
edger heatmap clustering differential gene expression rnaseq
updated 7.6 years ago by 53k • written 7.6 years ago by ▴ 60
4
votes
6
replies
7.3k
views
Using RPKM data in bioconductor for gene expression analysis
rpkm/fpkm differential gene expression
updated 10.3 years ago by 68k • written 10.3 years ago by ▴ 110
1
vote
7
replies
7.3k
views
featureCounts creating fragments and high NoFeatures value
featurecounts bioconductor differential gene expression star
updated 9.0 years ago by ★ 3.6k • written 9.0 years ago by ▴ 10
5
votes
9
replies
7.3k
views
how to control age and gender effect in expression data using DESeq2
deseq2 rnaseq mirna-seq differential gene expression
written 7.9 years ago by ▴ 20
9
votes
5
replies
7.0k
views
Finding DE genes from RNA-seq data
edgeR pvalue qvalue fpkm differential gene expression
updated 7.2 years ago by ★ 13k • written 7.2 years ago by • 0
7
votes
8
replies
7.0k
views
Only one replicate: inferring dispersion from other group
deseq2 edger limma differential gene expression
updated 11.1 years ago by 53k • written 11.1 years ago by ▴ 30
1
vote
10
replies
6.8k
views
DESEQ2: apparently wrong log2(fold-change) calculation
deseq2 differential gene expression log2fc
9.8 years ago Osvaldo ▴ 40
0
votes
8
replies
6.7k
views
Comparing between two differential expression analysis - two different fold changes
Deseq deseq2 differential gene expression rnaseq statistical test
7.9 years ago Marina ▴ 40
20
votes
18
replies
6.5k
views
Using of limma moderated t-test with "corrected" expression matrix resulting from ComBat batch effect correction
limma batch effect ComBat differential gene expression
updated 10.3 years ago by ▴ 870 • written 10.3 years ago by ▴ 840
6
votes
12
replies
6.5k
views
DESEq2 - Why is "my gene" not differentially expressed?
deseq2 differential gene expression
9.8 years ago Jane Merlevede ▴ 90
7
votes
9
replies
6.4k
views
LIMMA: interpreting interaction terms in an unbalanced factorial design with repeated measures
LIMMA FACTORIAL REPEATED MEASURES differential gene expression
10.4 years ago • updated 10.2 years ago robert.maughan • 0
5
votes
12
replies
6.4k
views
Differential expression analysis: comparison of DESeq2 and edgeR robust results
deseq2 edgeR differential gene expression
updated 9.7 years ago by ★ 29k • written 9.7 years ago by ▴ 90
3
votes
5
replies
6.2k
views
How to deal with low-depth RNA-Seq within DESeq2 or edgeR
rnaseq normalization differential gene expression edger deseq2
updated 8.9 years ago by ★ 7.9k • written 8.9 years ago by ▴ 90
3
votes
2
replies
6.2k
views
DESEQ2 Experimental Design
deseq2 differential gene expression
11.0 years ago fabiola • 0
1
vote
3
replies
6.2k
views
DESeq2 estimateSizeFactors with control genes
deseq2 differential gene expression controls references
updated 9 months ago by • 0 • written 7.1 years ago by • 0
9
votes
10
replies
5.9k
views
Simple significance test functions from R packages limma and plsgenomics
limma plsgenomics microarray differential gene expression
updated 11.0 years ago by 53k • written 11.0 years ago by ▴ 10
0
votes
7
replies
5.9k
views
Visualization of rownames in the heatmap.2 function for selected DE genes of a microarray dataset
heatmap.2 gplots differential gene expression visualization
10.8 years ago svlachavas ▴ 840
10
votes
4
replies
5.8k
views
Filtering lowly expressed genes in voom-limma analysis
voom limma rna-seq differential gene expression
updated 9.5 years ago by 53k • written 9.5 years ago by ▴ 110
1
vote
7
replies
5.6k
views
deseq2 analysis with multiple factors and interaction terms
deseq2 multiple factor design differential analysis differential gene expression
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 10
10
votes
13
replies
5.5k
views
Trouble identifying differentially expressed genes on Affymetrix Human Gene 2.0.ST using R with oligo and limma package
R limma oligo differential gene expression affymetrix microarrays
updated 10.5 years ago by • 0 • written 10.5 years ago by ▴ 10
2
votes
8
replies
5.5k
views
MDS Plot help in edgeR
edgeR plotmds differential gene expression MDS mdsplot
updated 7.0 years ago by 53k • written 7.0 years ago by • 0
6
votes
19
replies
5.3k
views
Time course analysis in DESeq2: handling common baseline for two experimental conditions
deseq2 timecourse multiple factor design RNAseq analysis differential gene expression
updated 8.3 years ago by ▴ 690 • written 8.3 years ago by ▴ 50
0
votes
13
replies
5.2k
views
DESeq2: collapseReplicates error
deseq2 rnaseq differential gene expression
9.4 years ago ta_awwad ▴ 10
3
votes
19
replies
5.1k
views
remove batch effect and adjusted model for 4 covariates in Limma
limma batch effect covariates contrast differential gene expression
8.8 years ago mheydarpour ▴ 10
1
vote
4
replies
5.0k
views
Running DESeqDataSet with 4 factors?
summarizedexperiment deseq2 deseqdataset multiple factor design differential gene expression
10.5 years ago Lillyhchen ▴ 10
0
votes
7
replies
4.9k
views
Deciding on cooks cutoff value DESeq2
deseq2 differential gene expression outliers bioconductor
updated 9.0 years ago by 43k • written 9.0 years ago by ▴ 10
7
votes
18
replies
4.9k
views
RNA-seq analysis using EdgeR- I need to make sure that the codes that I use to analyze the data are correct
rnaseq edger differential gene expression
updated 9.8 years ago by ★ 7.9k • written 9.8 years ago by • 0
5
votes
2
replies
4.8k
views
deseq2 LRT vs Wald test results for DE expression among 4 conditions
rnaseq deseq2 lrt wald differential gene expression
updated 3.8 years ago by • 0 • written 8.3 years ago by • 0
0
votes
2
replies
4.7k
views
Calculate correlation matrix for gene expression data
R differential gene expression
updated 8.8 years ago by • 0 • written 8.8 years ago by • 0
6
votes
4
replies
4.7k
views
Merge different datasets and perform differential expression analysis in limma
insilicomerging batcheffect limma differential gene expression bioconductor
updated 10.5 years ago by ★ 29k • written 10.5 years ago by ▴ 840
2
votes
5
replies
4.6k
views
processing data with 2 rep or one replicate by ballgown
ballgown differential gene expression
updated 9.2 years ago by ▴ 210 • written 9.3 years ago by • 0
0
votes
2
replies
4.5k
views
DESeq2 followed by goseq GO-analysis: Extracting DE genes of enriched GO category
deseq2 goseq rnaseq go enrichment differential gene expression
updated 7.9 years ago by 43k • written 7.9 years ago by • 0
6
votes
13
replies
4.4k
views
DEseq2 with limited gene set
DEseq2 differential gene expression
9.4 years ago dmr210 • 0
5
votes
9
replies
4.3k
views
Merge different datasets regarding a common number of DE genes in R
bioconductor expresiondataset affymetrixchip differential gene expression
10.9 years ago • updated 10.8 years ago svlachavas ▴ 840
1
vote
5
replies
4.3k
views
Contrast All Interaction Effects in DESeq2 in current version (1.10.1)
DESeq2 differential gene expression interactions
10.2 years ago marcus.stoiber • 0
3
votes
4
replies
4.2k
views
Simultaneously adding two different covariates in the model gives error in DESeq2.
deseq2 dexseq rnaseq differential gene expression differential exon usage
updated 9.0 years ago by 43k • written 9.0 years ago by ▴ 40
5
votes
6
replies
4.2k
views
Differential expression analysis - additive genetic model (how to implement it)
deseq2 edger differential gene expression additive model
10.1 years ago • updated 10.0 years ago jlerga • 0
4
votes
17
replies
4.1k
views
Question about decideTests function and adj.p.value in "limma" R Package
limma r differential gene expression
updated 8.5 years ago by 53k • written 8.5 years ago by ▴ 120
272 results • Page 1 of 6
Recent ...
Replies
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
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
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Awards • All
Popular Question to Stephanie M. Gogarten ▴ 890
Autobiographer to Frances Turner ▴ 20
Popular Question to maltethodberg ▴ 180
Popular Question to mohammedtoufiq91 ▴ 10
Popular Question to Lluís Revilla Sancho ▴ 760
Locations • All
Barcelona, Spain, 10 minutes ago
Seattle, WA, United States, 32 minutes ago
United States, 47 minutes ago
The Netherlands, 1 hour ago
United States, 1 hour ago
Traffic: 925 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