Showing : EdgeR • reset
2
votes
8
replies
2.5k
views
Differential gene expression using edgeR and using a generalised linear model (GLM)
edger GLM
updated 6.4 years ago by ★ 29k • written 6.4 years ago by • 0
2
votes
4
replies
1.2k
views
Why the result of pairwise comparison and Anova comparison of the same contrast is different ?
edger
updated 6.4 years ago by 53k • written 6.4 years ago by ▴ 10
1
vote
1
reply
1.6k
views
Meaning of edgeR decideTestsDGE values
edger
updated 6.4 years ago by 53k • written 6.4 years ago by • 0
1
vote
2
replies
1.2k
views
Call DE genes on Unbalanced design with controls
edger experimental design
6.4 years ago timedreamer ▴ 10
5
votes
5
replies
4.4k
views
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
limma edger
updated 6.4 years ago by 53k • written 6.4 years ago by ▴ 40
2
votes
4
replies
6.0k
views
edgeR and batch effect correction for differential analysis
edger limma r rnaseq batcheffect
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
1
vote
6
replies
2.3k
views
edgeR removing batch effect before using expression data for clustering
edger r batcheffect clustering removeBatchEffect
updated 6.4 years ago by 68k • written 6.4 years ago by ▴ 120
1
vote
2
replies
1.0k
views
Regarding error in Trinity edgeR calculation
edger
updated 6.4 years ago by 53k • written 6.4 years ago by • 0
1
vote
4
replies
1.7k
views
Complex Design matrix for DE analysis
deseq2 edger limma
updated 6.4 years ago by 43k • written 6.4 years ago by • 0
8
votes
5
replies
4.9k
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 6.4 years ago by 53k • written 6.4 years ago by ▴ 120
0
votes
2
replies
1.3k
views
How to create design matrix for differential analysis within the same cell-line samples?
edger r differentialanalysis rnaseq designmatrix
updated 6.5 years ago by ★ 29k • written 6.5 years ago by ▴ 60
1
vote
3
replies
1.2k
views
edgeR for looking at differences in coverage?
edgeR exome
updated 6.5 years ago by ★ 29k • written 6.5 years ago by • 0
3
votes
3
replies
2.9k
views
edgeR: Strange volcano plot
edger scRNA-seq DGEA
updated 6.5 years ago by ★ 29k • written 6.5 years ago by • 0
0
votes
5
replies
2.7k
views
EdgeR: Filtering Counts Causes No Significance.
edger
updated 4.6 years ago by • 0 • written 6.5 years ago by • 0
2
votes
5
replies
3.3k
views
MDS plot; Batch effects
limma rna-seq edger batches
updated 6.5 years ago by ★ 29k • written 6.5 years ago by • 0
0
votes
1
reply
793
views
Help with edgeR
edger
updated 6.5 years ago by 53k • written 6.5 years ago by ▴ 10
4
votes
7
replies
1.8k
views
EdgeR between/within comparisons (3.5) with nested non-balanced data set
edgeR nested glm glmQLFit
updated 6.5 years ago by ★ 29k • written 6.5 years ago by ▴ 10
3
votes
3
replies
1.7k
views
Voom shows error message:
Limma voom edger
updated 6.5 years ago by 53k • written 6.5 years ago by • 0
2
votes
6
replies
2.2k
views
EdgeR glmTreat error
edger error
updated 6.5 years ago by 68k • written 6.5 years ago by • 0
0
votes
2
replies
2.4k
views
create DGElist Object
edger DGElist
updated 6.5 years ago by 53k • written 6.5 years ago by • 0
0
votes
0
replies
977
views
Paired DE analysis in edgeR with trios of samples while blocking for various confounders
edger rnaseq paired analysis design matrix
6.5 years ago svlachavas ▴ 840
6
votes
7
replies
1.8k
views
Appropriate experimental design for differential expresion
edgeR normalization cancer
updated 6.6 years ago by ★ 1.4k • written 6.6 years ago by ▴ 30
3
votes
4
replies
1.5k
views
RNA-seq Statstical Models and Transcriptional Amplification
edgeR DESeq2 Transcriptional Amplification
updated 6.6 years ago by ★ 29k • written 6.6 years ago by ★ 1.6k
3
votes
5
replies
2.0k
views
Experimental design RNAseq differential expression
edger limma design contrasts batch
updated 6.6 years ago by ★ 29k • written 6.6 years ago by ▴ 40
1
vote
3
replies
3.4k
views
ENSEBL gene_ID in edgeR analysis
edgeR ENEMBL RefSeq
updated 6.6 years ago by 53k • written 6.6 years ago by • 0
0
votes
4
replies
2.2k
views
How to analyze RNAseq data with multiple treatment groups and each subject has pre and post-treatment measures using deseq2/edger/limma?
deseq2 limma edger Tutorial
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
4
votes
3
replies
1.9k
views
subset samples for RNAseq differential analysis
edger rnasq limma
updated 6.6 years ago by ★ 29k • written 6.6 years ago by • 0
1
vote
2
replies
1.2k
views
edgeR design matrix not of full rank
edger
updated 6.6 years ago by ★ 29k • written 6.6 years ago by • 0
0
votes
2
replies
1.0k
views
using limma for circular RNA analyses
limma R edger
updated 6.6 years ago by ★ 29k • written 6.6 years ago by • 0
0
votes
1
reply
2.1k
views
Dependence of FDR and P-values on sample size
edgeR FDR p-value Benjamini-Hochberg Differential Analysis
updated 6.6 years ago by ★ 29k • written 6.6 years ago by • 0
3
votes
4
replies
1.8k
views
Paired analysis (tumor vs normal) at three different conditions with EdgeR
edger design matrix de
updated 6.6 years ago by ★ 29k • written 6.6 years ago by ▴ 10
0
votes
0
replies
1.2k
views
I am trying to recreate results from an Alzheimer's paper but I can't figure out my linear regression model
limma microarray differential gene expression linear regression edger
6.6 years ago ravelarvargas • 0
3
votes
7
replies
1.2k
views
edgeR: request for additional guidelines for responsible limiting of genes that can be analyzed statistically
edger
updated 6.6 years ago by 53k • written 6.6 years ago by • 0
0
votes
4
replies
1.4k
views
Batch effect and edgeR analysis
batch effect edgeR RNA-seq
updated 6.6 years ago by 53k • written 6.6 years ago by ▴ 20
1
vote
2
replies
2.2k
views
Biological coefficient of variation(BCV) calculation in edgeR
edger bcv edgeR
updated 6.6 years ago by ★ 29k • written 6.6 years ago by • 0
1
vote
4
replies
1.7k
views
I am having trouble recreating the linear regression results published in an Alzheimer's paper
limma edger linear regression microarray differential gene expression
6.6 years ago ravelarvargas • 0
2
votes
10
replies
3.9k
views
Time-series analysis with DESeq2
deseq2 time-series design matrix edger
updated 6.7 years ago by 43k • written 6.7 years ago by ★ 1.5k
2
votes
6
replies
1.6k
views
Making sense out of makeContrasts and using coefficents for contrasts
edger contrasts
updated 6.7 years ago by 53k • written 6.7 years ago by • 0
4
votes
4
replies
3.1k
views
RNA-seq batch correction using technical replicates profiled across batches
deseq2 ruvseq sva edger limma
updated 6.7 years ago by 53k • written 6.7 years ago by ▴ 680
8
votes
4
replies
3.3k
views
edgeR /DESeq2 normalization for differential expression in RNA-seq blood samples
hemoglobin edgeR deseq2 normalization rnaseq
updated 6.7 years ago by ★ 7.9k • written 6.7 years ago by ▴ 90
0
votes
1
reply
1.1k
views
differentail expression analysis with interaction terms
edger deseq2 interaction design matrix
updated 6.7 years ago by 68k • written 6.7 years ago by ★ 1.5k
5
votes
3
replies
1.1k
views
Conduct likelihood ratio tests for a variable that isn't explicitly defined by matrix.model
edger
updated 6.7 years ago by 53k • written 6.7 years ago by • 0
1
vote
3
replies
804
views
How do you obtain the R - squared value from the NB line produced in plotMeanVar ?
edger rnaseq R
updated 6.7 years ago by 53k • written 6.7 years ago by • 0
6
votes
8
replies
3.8k
views
Use of pseudoalignment estimated counts as input to edgeR and Limma-Voom
RNASeq-quantification edgeR TPM
updated 6.7 years ago by 53k • written 6.7 years ago by ▴ 30
1
vote
5
replies
1.7k
views
My linear regression model is giving me too many differentially expressed genes
limma rna-seq differential gene expression edger linear regression
updated 6.7 years ago by ★ 29k • written 6.7 years ago by • 0
2
votes
5
replies
2.3k
views
edgeR or wilcoxon rank test? Which is right?
edgeR r wilcox RNA-seq cancer
6.7 years ago AZ ▴ 30
2
votes
6
replies
1.6k
views
Differential expression analysis error
edger
updated 6.7 years ago by 53k • written 6.7 years ago by • 0
1
vote
8
replies
2.1k
views
how can I calculate FDR with no replicate
microarray edger
updated 6.7 years ago by 53k • written 6.7 years ago by ▴ 30
1
vote
2
replies
1.2k
views
EdgeR -- differentially expressed genes across a continuous variable
edger continuous regression
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
3
votes
7
replies
1.7k
views
Different results with DESeq2 and EdgeR
desEQ2 edger
6.7 years ago AZ ▴ 30
2,031 results • Page 13 of 41
Recent ...
Replies
Comment: gene Set with high AUC score but no cells assigned to cell type by eja.hdrer33ge.r.m • 0
Understanding complex data results like those from AUCell can be challenging. For easier analysis and better data management on the go you …
Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by ubjw24 • 0
Thank you for your replies. I got the problem solved by installing mutSignature with this line: ``` devtools::install_github("dami82/mutS…
Comment: DESeq2 design for haplotype MPRA by Rita • 0
Thank you very much, I appreciate it!
Answer: DESeq2 design for haplotype MPRA by Michael Love 43k
> My goal is to identify which non-reference haplotypes are differentially active compared to the corresponding ref/ref haplotype within ea…
Answer: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k
It seems fine on devel as well. ``` > BSgenome.Hsapiens.UCSC.hg38 | BSgenome object for Human | - organism: Homo sapiens | - provide…
Votes
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Awards • All
Popular Question to abaed • 0
Popular Question to ubjw24 • 0
Popular Question to Gordon Smyth 53k
Popular Question to Hervé Pagès 16k
Popular Question to shepherl 4.2k
Locations • All
WEHI, Melbourne, Australia, just now
United States, 1 hour ago
United States, 1 hour ago
United States, 1 hour ago
United States, 1 hour ago
Traffic: 749 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