Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
edger
•
reset
2
votes
3
replies
63
views
How to correctly adjust for gender in edgeR
design
glm
edgeR
updated 4 hours ago by
ATpoint
★ 4.1k • written 6 hours ago by
Guillermo
• 0
1
vote
3
replies
202
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
updated 19 hours ago by
Gordon Smyth
50k • written 1 day ago by
Ashley
• 0
4
votes
2
replies
613
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
12 days ago • updated 9 days ago
gene_bioconductor
▴ 10
0
votes
1
reply
169
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 12 days ago by
Gordon Smyth
50k • written 13 days ago by
z_bahari
• 0
1
vote
2
replies
199
views
Citation for edgeR user guide
edgeR
written 21 days ago by
k___
▴ 30
0
votes
2
replies
144
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
26 days ago
prity6459
• 0
0
votes
3
replies
207
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 26 days ago by
Gordon Smyth
50k • written 27 days ago by
prity6459
• 0
5
votes
3
replies
298
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 5 days ago by
Gordon Smyth
50k • written 27 days ago by
Shaimaa Gamal
• 0
4
votes
6
replies
457
views
FilterByExpr low counts with small sample size
edgeR
28 days ago • updated 23 days ago
Jonathan
▴ 10
1
vote
3
replies
364
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 4 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Simran
• 0
5
votes
6
replies
451
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 4 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
nhaus
▴ 30
3
votes
3
replies
362
views
permutation test in edgeR
rna-seq
edgeR
updated 24 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Netanel
• 0
1
vote
3
replies
274
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
Shaimaa Gamal
• 0
0
votes
2
replies
190
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
6 weeks ago
Marianna
▴ 20
0
votes
4
replies
443
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
6 weeks ago
Lucy
▴ 60
3
votes
5
replies
406
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Fabian
• 0
0
votes
6
replies
366
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Faisal
• 0
0
votes
1
reply
247
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
scoops_streams_06
• 0
5
votes
3
replies
729
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Jack S.
▴ 50
2
votes
3
replies
305
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
JKim
• 0
0
votes
2
replies
298
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
z_bahari
• 0
2
votes
2
replies
268
views
between lane normalization upper quantile
EDASeq
edgeR
8 weeks ago
elesofi
• 0
2
votes
2
replies
281
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
8 weeks ago
Sabiha
▴ 20
3
votes
4
replies
483
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 10 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
Jack S.
▴ 50
0
votes
1
reply
232
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 10 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
Fabian
• 0
0
votes
1
reply
274
views
ExactTest vs QLFTest
edgeR
updated 10 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
fr8712ca-s
• 0
0
votes
11
replies
764
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 10 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
mico
• 0
1
vote
6
replies
517
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
11 weeks ago
mico
• 0
5
votes
4
replies
418
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
12 weeks ago • updated 11 weeks ago
pl23
• 0
2
votes
6
replies
432
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
12 weeks ago
tsl0026
• 0
0
votes
8
replies
672
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
3 months ago • updated 12 weeks ago
Marianna
▴ 20
3
votes
2
replies
487
views
How does one test for interactions in EdgeR?
edgeR
3 months ago
pl23
• 0
0
votes
4
replies
361
views
Nested paired design
edgeR
3 months ago
manduchi
▴ 10
1
vote
2
replies
340
views
How to get normalized values for methylation counts in edgeR
edgeR
MethylationArray
3 months ago
mico
• 0
2
votes
3
replies
383
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
Shaimaa Gamal
• 0
1
vote
3
replies
435
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 3 months ago by
pl23
• 0
6
votes
7
replies
592
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
aa.machado001
• 0
1
vote
8
replies
565
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
sat
• 0
0
votes
0
replies
257
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
3 months ago
Jawahar
• 0
2
votes
4
replies
631
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
3 months ago
Sabiha
▴ 20
0
votes
3
replies
361
views
EdgeR for methylation analysis when there is no replicates
RRBSdata
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
annasoudi
• 0
3
votes
3
replies
699
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
Jurgen
• 0
4
votes
4
replies
448
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by
James W. MacDonald
65k • written 4 months ago by
Geo
• 0
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2
edgeR
4 months ago
Luca
• 0
0
votes
1
reply
318
views
download problem
edgeR
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
theokirkland3
• 0
0
votes
5
replies
637
views
Help with model for differential expression analysis
DifferentialExpression
edgeR
4 months ago • updated 3 months ago
Lucy
▴ 60
1
vote
2
replies
487
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
4 months ago
Sabiha
▴ 20
5
votes
2
replies
593
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
1
vote
2
replies
449
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression
edgeR
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
Jurgen
• 0
7
votes
2
replies
846
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Create protein sequences including variants from a VCF file
by
Yun
• 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization?
by
Daniel
• 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Guido Hooiveld
★ 4.0k
FWIW: based on [previous posts][1] it is suggested to install like this: install.packages(pkgs="./org.Vdahliae.eg.db", repos=NULL, typ…
Votes
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
Answer: How to design DEXSeq formula for multiple variables
Awards
• All
Popular Question
to
Vincent J. Carey, Jr.
6.7k
Popular Question
to
boczniak767
▴ 720
Popular Question
to
jmoon1194
• 0
Popular Question
to
mat.lesche
▴ 90
Popular Question
to
jordi.planells
• 0
Locations
• All
France,
just now
India,
4 minutes ago
United States,
6 minutes ago
United States,
10 minutes ago
UPF, Barcelona, Spain,
11 minutes ago
Traffic: 799 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