Showing : edgeR • reset
1
vote
1
reply
1.4k
views
cpm filtering parameter
cpm filtering transcriptomics rnaseq edgeR metatranscriptomics
updated 6.2 years ago by 53k • written 6.2 years ago by ▴ 10
5
votes
6
replies
1.9k
views
is our edgeR code doing what we think it does?
edger differential expression rna-seq
updated 6.2 years ago by ▴ 900 • written 6.2 years ago by ▴ 10
0
votes
1
reply
2.1k
views
Different Expression Analysis with EDASeq,DESeq2,edgeR,RUVSeq
deseq2 normalization RUVg edger
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
2
votes
3
replies
1.6k
views
Design for introducing batch effect in DESeq2
deseq2 combat batch effect rna-seq edger
updated 6.2 years ago by ★ 1.4k • written 6.2 years ago by ▴ 80
0
votes
2
replies
1.8k
views
How an index is built for each gene set collections using buildCustomIdx() indexing function of EGSEA package?
EGSEA edgeR biomaRt limma RNA-seq
6.2 years ago fgol ▴ 10
0
votes
2
replies
693
views
Searching for responsive genes along with a continuous variable, in environmental experimental design
edger
updated 6.2 years ago by 53k • written 6.2 years ago by • 0
2
votes
1
reply
1.3k
views
edgeR default normalization method
edger
updated 6.2 years ago by 53k • written 6.2 years ago by • 0
1
vote
6
replies
2.9k
views
Use intercept or not in model matrix for edgeR methylation analysis
edgeR R methylation GLM
6.2 years ago sabrina.mcnew • 0
1
vote
1
reply
1.6k
views
Using `catchSalmon()` to import Salmon counts quantified using a decoy-aware transcriptome index
edgeR Salmon
6.2 years ago konstantinos.bogias ▴ 10
0
votes
4
replies
949
views
The meaning of interaction terms in design matrix in edgeR User's Guide on page 38
edger
updated 6.3 years ago by 53k • written 6.3 years ago by • 0
0
votes
1
reply
449
views
Sai Nikhith Cholleti
edger deseq2
updated 6.3 years ago by 43k • written 6.3 years ago by • 0
0
votes
6
replies
2.4k
views
analysis of multiple batches and multiple treatment conditions in scRNA-seq
limma deseq2 edger scRNAseq combat
updated 6.3 years ago by ▴ 280 • written 6.3 years ago by ▴ 670
1
vote
4
replies
1.1k
views
Is the colnames of model.matrix on the page 34 in edgeR User's Guide?
edger
updated 6.3 years ago by 53k • written 6.3 years ago by • 0
2
votes
2
replies
1.5k
views
How to create two columns for model matrix used in limma?
limma edger
updated 6.3 years ago by 53k • written 6.3 years ago by ▴ 60
8
votes
5
replies
5.4k
views
the normalization methods of MRN and TMM methods supplied by DESeq2 and edgeR
normalization DESeq2 edgeR
updated 6.3 years ago by 53k • written 6.3 years ago by ▴ 10
7
votes
4
replies
3.1k
views
RNA-seq normalization without filtering
deseq2 edger normalization RNAseq
updated 6.3 years ago by ★ 13k • written 6.3 years ago by ▴ 50
1
vote
5
replies
4.6k
views
how to get normalized count data from edgeR using TMM methods
edger normalization
6.3 years ago 15958021290 ▴ 10
0
votes
4
replies
1.4k
views
design matrix for 4 groups in edgeR
edger
updated 6.3 years ago by 53k • written 6.3 years ago by • 0
0
votes
0
replies
932
views
News: Course in Berlin- Genomics with R and Bioconductor - September 16-20
deseq2 edger limma News
6.3 years ago info ▴ 10
0
votes
4
replies
4.8k
views
edgeR DGEList and design matrix
edger DGE
updated 6.3 years ago by ▴ 900 • written 6.3 years ago by • 0
0
votes
3
replies
1.1k
views
Most (90%) DE genes of a contrast were upregulated: implication on the assumptions of TMM-normalisation?
limma edger normalization
updated 6.3 years ago by 53k • written 6.3 years ago by ▴ 280
0
votes
4
replies
3.0k
views
EdgeR mistake- dispersion
edger
updated 6.3 years ago by 53k • written 6.3 years ago by • 0
6
votes
10
replies
6.6k
views
goana and "No annotated genes found in universe" even with Entrez gene ids
goana edger
updated 3.8 years ago by 53k • written 6.3 years ago by ▴ 10
4
votes
4
replies
3.6k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
updated 6.3 years ago by ★ 29k • written 6.3 years ago by ▴ 670
4
votes
4
replies
1.3k
views
normalization of RNA-seq data after over-expressing the transcription factors
limma deseq2 voom edgeR
updated 6.3 years ago by ★ 29k • written 6.3 years ago by ▴ 670
1
vote
4
replies
1.2k
views
Feedback on edgeR model setup: identifying sex-by-tissue effects
edger
updated 6.3 years ago by ★ 29k • written 6.3 years ago by • 0
2
votes
6
replies
2.7k
views
RNA-Seq normalization for co-expression analysis
edger WGCNA limma
updated 6.4 years ago by 53k • written 6.4 years ago by ▴ 50
6
votes
6
replies
1.5k
views
EdgeR - Model matrix for complex model similar to user guide 3.5 example - but more complex
edger limma
updated 6.4 years ago by 68k • written 6.4 years ago by ▴ 10
5
votes
18
replies
2.7k
views
Difference of difference, paired design
edger deseq2 limma
updated 6.4 years ago by ★ 1.4k • written 6.4 years ago by • 0
1
vote
4
replies
1.5k
views
Creating contrasts which do not include the reference level in limma, edgeR or DESeq2
limma deseq2 edgeR
updated 6.4 years ago by 68k • written 6.4 years ago by ▴ 50
0
votes
0
replies
1.1k
views
adding batch effects as a covariate in additive model in edgeR
edger batch effects
updated 6.4 years ago by 68k • written 6.4 years ago by • 0
4
votes
3
replies
1.4k
views
Complex multifactorial design with random effects in Limma/voom
limma edger
updated 6.4 years ago by ★ 29k • written 6.4 years ago by ▴ 20
0
votes
4
replies
3.0k
views
Why am I getting many differentially expressed genes that have no symbol or do not map to a chromosome (RNA-seq)
edger
updated 6.4 years ago by 53k • written 6.4 years ago by • 0
3
votes
3
replies
2.5k
views
Differential Expression Analysis in edgeR using Anova
edger anova gene expression Dispersion
updated 6.4 years ago by • 0 • written 6.8 years ago by • 0
0
votes
3
replies
868
views
FNR in RNASeq
deseq2 edger
updated 6.4 years ago by 53k • written 6.4 years ago by • 0
0
votes
2
replies
2.5k
views
Normalized count in edger
edger
updated 6.4 years ago by ▴ 10 • written 6.4 years ago by • 0
2
votes
4
replies
1.9k
views
Majority upregulated genes in edgeR
edger differential expression genes fold change
updated 6.4 years ago by ★ 29k • written 6.4 years ago by • 0
1
vote
6
replies
3.2k
views
adjusting for confounding effects in edgeR
edger confounding
updated 6.4 years ago by ★ 29k • written 6.4 years ago by • 0
5
votes
3
replies
1.9k
views
Combining counts from non-replicate samples in RNA-Seq analysis for a synergistic system
edger normalization counts RNA-seq
updated 6.4 years ago by ★ 29k • written 6.4 years ago by • 0
8
votes
7
replies
2.7k
views
Confounded design, batch effect correction (edgeR)
rnaseq edger differential gene expression batch effect
updated 6.4 years ago by • 0 • written 7.2 years ago by ▴ 20
1
vote
5
replies
2.0k
views
bug in "dispersion" argument in edgeR - rpkmByGroup
edger rpkm
updated 6.4 years ago by • 0 • written 6.4 years ago by • 0
5
votes
3
replies
1.7k
views
Re-numbering blocking IDs on paired samples with duplicateCorrelation or design covariate
edger limma duplicateCorrelation batch effect
updated 6.4 years ago by ★ 29k • written 6.4 years ago by • 0
6
votes
8
replies
2.5k
views
How to find out the genes that changes in expression by using gene level expression data matrix?
limma microarray affy edger
6.4 years ago Jurat Shahidin ▴ 80
3
votes
7
replies
4.5k
views
How to determine the cause of no difference between treatments in rnaseq?
RNAseq DGE edger
updated 6.4 years ago by 53k • written 6.4 years ago by • 0
1
vote
12
replies
2.1k
views
RNA-Seq and edgeR: remarkable differences between cpms and fitted values
RNA-Seq edger fitted values differential expression normalization
updated 6.4 years ago by 53k • written 6.4 years ago by ▴ 90
0
votes
0
replies
1.3k
views
Incorporating factors of unwanted variation from RUVr into EdgeR cell means model for DE
edger RUVseq RUVr GLM RNAseq
6.4 years ago garbuzov • 0
0
votes
2
replies
3.2k
views
Error: row names supplied are of the wrong length in RUVSeq
RUVSeq software error edger
updated 6.5 years ago by ▴ 980 • written 6.6 years ago by • 0
0
votes
3
replies
1.5k
views
phyloseq to edgeR
edger
updated 6.5 years ago by 53k • written 6.5 years ago by ▴ 10
0
votes
1
reply
592
views
Test genes expressed ( not just expressed higher ) in one or two group
limma edger
updated 6.5 years ago by 53k • written 6.5 years ago by ▴ 30
5
votes
7
replies
3.6k
views
logCPM to CPM conversion after removeBatchEffect()
edger removeBatchEffect cpm logCPM limma
6.5 years ago altintas.ali • 0
2,031 results • Page 12 of 41
Recent ...
Replies
Comment: Error installing Seqinfo by shepherl 4.2k
Yes and we are working on getting the updated windows binaries distributed asap! We are hopeful by the end of this week
Comment: APAlyzer by shepherl 4.2k
We apologize for their unresponsiveness; you could try posting your question here to see if anyone in the community could assist in the me…
Answer: Error installing Seqinfo by fabio.marroni • 0
I am answering my own question. I found the solution thanks to [this post][1], and I am writing here the very simple procedure: 1) Instal…
Comment: Getting a large intercept with DESeq2 by Michael Love 43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k
As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…
Votes
Comment: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Issues with downloading biomaRt - SeqInfo and S4 Vectors
Comment: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Awards • All
Popular Question to James W. MacDonald 68k
Popular Question to anjanaram1 ▴ 10
Popular Question to Gordon Smyth 53k
Popular Question to Stephen Piccolo ▴ 600
Popular Question to Maria Doyle ▴ 100
Locations • All
Australia, 10 minutes ago
Germany, 24 minutes ago
United States, 29 minutes ago
Chile, 31 minutes ago
United States, 49 minutes ago
Traffic: 825 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