Showing : EdgeR • reset
1
vote
9
replies
4.6k
views
Spike-in normalization in EdgeR
CUTandRUN edgeR Normalization SpikeIn ChIPSeq
updated 2.9 years ago by ▴ 670 • written 5.0 years ago by ▴ 10
0
votes
1
reply
639
views
Using DESEQ/EdgeR for estimating differential expression relative to a control.
edgeR DifferentialExpression
updated 4.9 years ago by 43k • written 5.0 years ago by • 0
0
votes
1
reply
898
views
edgeR rrbs estimateDisp runs forever and doesn't seem to finish
edgeR
updated 5.0 years ago by 53k • written 5.0 years ago by • 0
1
vote
1
reply
2.0k
views
DiffBind for ATAC-Seq count extraction
esATAC edgeR DiffBind
updated 5.0 years ago by ★ 5.2k • written 5.0 years ago by • 0
2
votes
2
replies
1.2k
views
log transform or not the dependent variable/ covariates
limma edgeR
updated 5.0 years ago by 53k • written 5.0 years ago by ▴ 40
4
votes
10
replies
2.0k
views
Paired Time course Experiment Design on edgeR between and within groups
edgeR diffcyt limma DifferentialExpression
5.0 years ago Hajar • 0
2
votes
2
replies
1.2k
views
Paired analysis adjusted for RIN value
limma edgeR
updated 5.0 years ago by 53k • written 5.0 years ago by ▴ 40
4
votes
3
replies
2.4k
views
catchSalmon for tx-level DE
catchSalmon edgeR
updated 23 months ago by 53k • written 5.0 years ago by ★ 5.0k
9
votes
10
replies
9.6k
views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
Normalization edgeR RPKM
updated 2.6 years ago by ▴ 20 • written 5.0 years ago by ▴ 10
1
vote
0
replies
633
views
Differential gene expression associated with metabolite levels following diet
edger
5.0 years ago anna.cot.anna.cot ▴ 40
1
vote
3
replies
909
views
filter factor DGEList
edger
updated 5.0 years ago by 53k • written 5.0 years ago by • 0
2
votes
3
replies
1.3k
views
EdgeR design matrix for mutlifactor RNA seq
edger design multifactor
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
2
votes
7
replies
3.6k
views
EdgeR diffSpliceDGE: Obtaining exon-level counts and normalisation step
edger normalization differential exon usage splicing
updated 5.0 years ago by ▴ 900 • written 5.0 years ago by • 0
0
votes
2
replies
1.8k
views
edgeR for single-cell data with inferential replicates
edgeR alevin
5.0 years ago ATpoint ★ 5.0k
2
votes
5
replies
1.9k
views
How should I handle read counts derived from SGSeq when they were passed to limma/edgeR
SGSeq limma edgeR
updated 13 months ago by • 0 • written 5.0 years ago by ▴ 10
0
votes
8
replies
1.8k
views
Designating contrasts in diffSpliceDGE to test for nested effects
diffSpliceDGE Contrast matrix edger
updated 5.0 years ago by 53k • written 5.0 years ago by • 0
3
votes
3
replies
1.5k
views
Problem to understand Interactions at any time
RNA-seq edgeR interactions
updated 5.0 years ago by 53k • written 5.0 years ago by ▴ 10
1
vote
1
reply
813
views
In edgeR, how am I supposed to be gauging the results of the BCV Plots, the values of common dispersion, tagwise disperson, ect.
edger
5.0 years ago science555111 • 0
10
votes
10
replies
2.4k
views
RNA-Seq analysis with Limma/edgeR, time course experiment, aberrant results
limma edger
updated 5.0 years ago by 68k • written 5.0 years ago by ▴ 10
3
votes
1
reply
1.2k
views
How do you create a targets dataframe in edgeR?
edgeR RNA-SEQ
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
5
votes
2
replies
952
views
Differential gene expression associated with change in blood parameter following diet
edger
updated 5.1 years ago by 53k • written 5.1 years ago by ▴ 40
6
votes
4
replies
1.4k
views
edgeR and batch effects
edger
updated 5.1 years ago by ★ 13k • written 5.1 years ago by ▴ 10
6
votes
5
replies
2.4k
views
Calculating standard deviation for a few genes using RNAseq data
edger RNAseq
updated 5.1 years ago by ★ 13k • written 5.1 years ago by • 0
3
votes
6
replies
1.5k
views
EdgeR design matrix with 3 factors
edgeR glm RNAseq
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
1
vote
1
reply
783
views
technical replicates in WGCNA
edger
updated 5.1 years ago by ★ 3.0k • written 5.1 years ago by • 0
9
votes
4
replies
1.7k
views
TMM normalization on sparse datasets
edger limma
5.1 years ago jc235601 ▴ 20
2
votes
4
replies
9.8k
views
Trying to do a PCA using edgeR with expression data
edger expression data pca
updated 5.1 years ago by 53k • written 5.1 years ago by • 0
1
vote
2
replies
1.3k
views
eisaR settings for three biological replicates
eisaR edgeR
updated 5.1 years ago by 53k • written 5.1 years ago by • 0
2
votes
2
replies
2.0k
views
RNA-Seq Time series analysis in EdgeR
edger Time series analysis
updated 5.1 years ago by 53k • written 5.1 years ago by ▴ 10
1
vote
3
replies
4.6k
views
TMM normalized matrix from count matrix using edgeR
edger
updated 5.1 years ago by 53k • written 5.1 years ago by • 0
0
votes
1
reply
658
views
do cox and km plot
limma edger
updated 5.1 years ago by ★ 4.0k • written 5.1 years ago by ▴ 20
0
votes
2
replies
1.0k
views
How to normalise data in ballgown?
r normalization edger
updated 5.1 years ago by 68k • written 5.1 years ago by • 0
0
votes
6
replies
1.2k
views
The coefficients not estimable
edger
updated 5.1 years ago by 53k • written 5.1 years ago by ▴ 420
2
votes
4
replies
2.7k
views
Minimum required samples for RNA-seq differential Analysis?
deseq2 limma edger
5.1 years ago linouhao ▴ 20
0
votes
2
replies
4.2k
views
CPM function in EDGER
edger cpm rnaseq
5.1 years ago francesca3 • 0
0
votes
2
replies
808
views
Custom dispersion estimate DESeq2
deseq2 edger
updated 5.1 years ago by ★ 29k • written 5.1 years ago by ▴ 110
1
vote
7
replies
2.2k
views
problem recasting InteractionSet into a DGEList
diffHic GenomicInteractions edgeR HiC cooler
updated 5.1 years ago by ★ 29k • written 5.1 years ago by ▴ 30
6
votes
13
replies
7.7k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 3.2 years ago by 53k • written 5.1 years ago by ▴ 60
6
votes
4
replies
3.9k
views
Having TMM for GSEA
edger deseq2
updated 4.6 years ago by ★ 4.0k • written 5.2 years ago by ▴ 30
5
votes
8
replies
1.9k
views
Not seeing gene ID in glmQLFit headers
glmQLFit edgeR header
updated 5.2 years ago by 53k • written 5.2 years ago by • 0
0
votes
1
reply
941
views
Regression Analysis between RNA-seq data and expression measured from ELISA
limma edger
5.2 years ago Bioinformatician_R ▴ 20
2
votes
8
replies
2.7k
views
Differential gene expression using R
deseq2 edger normalization limma
updated 5.2 years ago by 53k • written 5.2 years ago by • 0
8
votes
11
replies
1.9k
views
Is there any model in EdgeR that is close to nested ANOVA?
edger rnaseq
updated 5.2 years ago by 53k • written 5.2 years ago by ▴ 10
2
votes
2
replies
905
views
Can edgeR be used to calculate the foldchange difference of GOs / KEGG terms/ Or even microbe abundance?
edger
5.2 years ago megha.hs28 ▴ 10
2
votes
2
replies
1.9k
views
Using EdgeR after importing transcript abundance (by SALMON) with tximport
edger normalization
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
2
votes
2
replies
1.3k
views
edgeR batch effect correction for unevenly distributed groups
rnaseq edgeR batch effect
updated 5.2 years ago by 53k • written 5.2 years ago by • 0
4
votes
3
replies
565
views
Average Effect in edgeR
edgeR
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
2
votes
2
replies
1.1k
views
In EdgeR TMM and/or voom is it better to normalize all samples, even if some will not be used for comparisons?
edger limma
updated 5.2 years ago by 53k • written 5.2 years ago by ▴ 60
2
votes
3
replies
2.5k
views
"Error in xy.coords(x, y, setLab = FALSE) : 'x' and 'y' lengths differ" using glmQLFit
glmQLFit edger
updated 5.2 years ago by 53k • written 5.2 years ago by • 0
4
votes
7
replies
1.7k
views
Genes upregulated in one condition vs each of the other conditions
edger design
updated 5.2 years ago by 53k • written 5.2 years ago by • 0
2,031 results • Page 9 of 41
Recent ...
Replies
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Awards • All
Popular Question to Michael Love 43k
Popular Question to Peter • 0
Popular Question to Travis • 0
Popular Question to James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Locations • All
United States, 1 hour ago
The city by the bay, 2 hours ago
Hong Kong, 5 hours ago
WEHI, Melbourne, Australia, 6 hours ago
Pittsburgh, United States, 8 hours ago
Traffic: 1440 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