Showing : edger • reset
0
votes
2
replies
919
views
suggest to report differential estimate in edgeR
edgeR
3.1 years ago • updated 3.0 years ago Yongqing • 0
0
votes
4
replies
1.3k
views
What function in edgeR normalize the reads between samples?
edgeR
3.1 years ago 冠宇 • 0
4
votes
5
replies
6.7k
views
How to identify top most variable genes from log2 normalized data?
supervised edgeR variance RNASeq heatmaps
updated 3.0 years ago by 53k • written 3.1 years ago by ▴ 10
2
votes
2
replies
1.1k
views
Inccorect group number in DGEList
edgeR Bioconductor Dseq2 dgelist
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
0
votes
0
replies
862
views
Installing edgeR on M1 mac
edgeR
3.1 years ago Onur • 0
0
votes
2
replies
917
views
I need help with EdgeR!
edgeR
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by • 0
0
votes
2
replies
1.5k
views
Analyzing barcode sequencing experiments with DESeq2/edgeR
edgeR DESeq2
updated 3.1 years ago by • 0 • written 3.6 years ago by • 0
0
votes
2
replies
1.4k
views
TnSeq as ZINB? Alternatives in R?
DESeq2 R edgeR Python TnSeq
updated 3.1 years ago by • 0 • written 3.2 years ago by ▴ 90
0
votes
0
replies
830
views
normFactors or calcNormFactors (computing the normalization or scaling factors)
limma edgeR csaw
3.1 years ago Bogdan ▴ 670
3
votes
6
replies
1.9k
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
3.1 years ago mohammedtoufiq91 ▴ 10
4
votes
6
replies
1.9k
views
Question on creating right design matrix in edgeR
R designmatrix edgeR limma model.matrix
3.1 years ago Abdul ▴ 20
5
votes
6
replies
3.6k
views
How to interpret Histogram of average log2 CPM filtering in EdgeR?
CPM filterByExpr edgeR histogram rowsums
3.1 years ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
1.3k
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
3.1 years ago mohammedtoufiq91 ▴ 10
0
votes
2
replies
2.4k
views
Getting this error while trying to use edgeR "Error in as.vector(x, mode) : cannot coerce type 'closure' to vector of type 'any'"
edgeR edge
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
0
votes
1
reply
1.6k
views
unable to load edgeR after installing it
edgeR
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by • 0
2
votes
4
replies
6.1k
views
Possibility of using TPM or FPKM values in edgeR for differential expression analysis?
DESeq2 R edgeR Normalization RNASeq
3.1 years ago mohammedtoufiq91 ▴ 10
1
vote
12
replies
3.9k
views
normalization of ChIP-seq data by using the spike-ins or by using total library sizes
DESeq2 edgeR limma
updated 3.1 years ago by 43k • written 3.2 years ago by ▴ 670
1
vote
3
replies
1.9k
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 3.1 years ago by 53k • written 3.2 years ago by • 0
3
votes
6
replies
2.2k
views
One-tailed test edgeR possible?
one-tailed edgeR DifferentialExpression test
written 3.2 years ago by • 0
2
votes
5
replies
1.8k
views
Can we massively improve RNA-Seq results by slightly reducing the counts in it?
edgeR RNAseq123
updated 3.1 years ago by 53k • written 3.2 years ago by ▴ 50
1
vote
2
replies
1.5k
views
How to process and analyze Total RNA-Seq data?
DESeq2 R edgeR Normalization RNASeq
3.2 years ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
1.6k
views
Trouble with importing transcript counts with Salmon
Salmon tximport RNAseq EdgeR
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
3
votes
6
replies
3.6k
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
3.2 years ago Sara • 0
0
votes
4
replies
1.7k
views
paired tests with tidybulk and edgeR
edgeR R tidyverse tidybulk
3.2 years ago Amit Indap ▴ 10
3
votes
7
replies
2.9k
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
2
votes
1
reply
1.1k
views
Different sequencing depth between replicates and samples
DESeq2 edgeR DiffBind
updated 3.2 years ago by 53k • written 3.2 years ago by ▴ 10
1
vote
4
replies
1.6k
views
RNA-seq analysis between a wildtype vs a double microRNA kockout mouse brain
microRNA gene RNASeqRData edgeR geneontology
3.2 years ago faiza • 0
2
votes
4
replies
1.7k
views
DiffBind and peak counts as input
DESeq2 edgeR DiffBind
updated 3.1 years ago by ★ 5.2k • written 3.3 years ago by ▴ 670
1
vote
7
replies
1.8k
views
statistics : edger or DESeq2 to asses the differential binding using the average scores
DESeq2 edgeR
updated 3.1 years ago by • 0 • written 3.3 years ago by ▴ 670
1
vote
1
reply
3.6k
views
installation of BioC packages on Mac M1 Monterrey OS
limma Bioconductor edgeR
3.3 years ago Bogdan ▴ 670
0
votes
1
reply
2.6k
views
bigwig to counts
DESeq2 edgeR bigwig limma
3.3 years ago • updated 3.0 years ago Bogdan ▴ 670
1
vote
4
replies
2.0k
views
QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM edgeR qsea MEDIPS
updated 3.3 years ago by • 0 • written 3.3 years ago by ▴ 20
0
votes
11
replies
5.7k
views
edgeR contrasts
edgeR
updated 2.4 years ago by 68k • written 3.4 years ago by • 0
3
votes
6
replies
2.2k
views
variance decomposition formula
edgeR
3.4 years ago Xinwei • 0
-6
votes
4
replies
1.3k
views
is it possible and reasonable for edgeR to derive DEGs from a complicated contrast or contrast of contrast?
complicated.contrast edgeR DEGs
3.4 years ago Mike • -60
1
vote
1
reply
917
views
How to interpret FC and pesudocounts in EDGER using glmLRT?
edgeR
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
0
votes
0
replies
919
views
Argument is of length zero in variancePartition/Dream
expression variancePartition edgeR
3.4 years ago Jonathan • 0
1
vote
4
replies
10.0k
views
TPM normalization starting with read counts
edgeR DESeq2
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
3
votes
4
replies
1.5k
views
edgeR processAmplicons not recognizing hairpin sequences
edgeR
updated 3.5 years ago by 53k • written 3.5 years ago by ▴ 10
1
vote
1
reply
1.4k
views
Filtering Orthologus Genes Before or After TMM normalization?
RNASeq Normalization TMM edgeR
updated 3.5 years ago by 53k • written 3.5 years ago by ▴ 10
3
votes
4
replies
3.8k
views
Why Negative value from GSVA
GSVA RNASeq edgeR
3.5 years ago Yang Shi ▴ 10
5
votes
8
replies
28k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 17 months ago by ▴ 60 • written 3.6 years ago by ▴ 30
1
vote
3
replies
3.2k
views
miRNA differential expression analysis - treat as transcript level?
tximport DESeq2 edgeR swish miRNA
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
0
votes
4
replies
3.8k
views
Confused about using RUVg in getting negative control genes using RUVg
RUVnormalize R edgeR RUVSeq RUVnormalizeData
3.6 years ago Mohamed ▴ 30
1
vote
8
replies
2.4k
views
edgeR design matrix with multiple cell types and combination treatments
DifferentialExpression celltype treatment edgeR limma
3.6 years ago giBio • 0
0
votes
1
reply
1.8k
views
dispersion in edgeR
Sequencing edgeR Sequencing edgeR
updated 3.6 years ago by 53k • written 15.6 years ago by ★ 6.0k
0
votes
2
replies
1.6k
views
Locating nearest genes in RRBS analysis
hiAnnotator bsseq DifferentialMethylation edgeR RRBSdata
3.7 years ago • updated 3.6 years ago Mageiros • 0
3
votes
2
replies
1.6k
views
time-series analysis using EdgeR
timecourse edgeR
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
2
votes
3
replies
3.1k
views
Confused about the design matrix in edgeR: How to tell R to consider one level as a reference and the other is a treatment to be compared to that ref.
R edgeR
updated 3.7 years ago by 53k • written 3.7 years ago by ▴ 30
2
votes
2
replies
1.4k
views
Help with constructing design matrix for edgeR/limma
limma design.matrix model.matrix edgeR
3.7 years ago • updated 3.6 years ago adrianna_07 • 0
2,035 results • Page 5 of 41
Recent ...
Replies
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Martin Morgan 25k
I see rstudioapi in the `sessionInfo()`. RStudio does not support forked ('multicore') processes. Does the BiocParallel example work when y…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
Given that this is an issue with BiocParallel on your machine and we have a minimal reproducible example, you may want to repost the issue.…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by ATpoint ★ 5.0k
Yes, still it's not reproducible, yet hard to debug. I cannot reproduce myself either.
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Benjamin • 0
Still happening using pre-existing size factors estimating dispersions gene-wise dispersion estimates: 15 workers mean-dis…
Answer: BiocParallel (and DESeq2) - wrong args for environment subassignment by Benjamin • 0
Still happening in a clean install
Votes
Comment: limpa analysis advice
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
Awards • All
Popular Question to Martin Morgan 25k
Teacher to Michael Love 43k
Popular Question to A • 0
Popular Question to Lluís Revilla Sancho ▴ 760
Popular Question to nromerov • 0
Locations • All
United States, 22 minutes ago
United States, 22 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
Melbourne, Australia, 1 hour ago
The city by the bay, 2 hours ago
Traffic: 1111 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