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EdgeR
•
reset
0
votes
0
replies
15
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
1 hour ago
Fabian
• 0
0
votes
1
reply
25
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
2 hours ago • updated 1 hour ago
Faisal
• 0
0
votes
1
reply
145
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 6 days ago by
Gordon Smyth
50k • written 7 days ago by
scoops_streams_06
• 0
4
votes
3
replies
401
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 23 hours ago by
Gordon Smyth
50k • written 7 days ago by
Jack S.
▴ 50
2
votes
3
replies
218
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 9 days ago by
Gordon Smyth
50k • written 10 days ago by
JKim
• 0
0
votes
2
replies
212
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 12 days ago by
Gordon Smyth
50k • written 13 days ago by
z_bahari
• 0
2
votes
2
replies
197
views
between lane normalization upper quantile
EDASeq
edgeR
14 days ago • updated 10 days ago
elesofi
• 0
2
votes
2
replies
188
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
14 days ago
Sabiha
▴ 20
0
votes
3
replies
306
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 8 weeks ago by
pl23
• 0
3
votes
4
replies
287
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 22 days ago by
Gordon Smyth
50k • written 23 days ago by
Jack S.
▴ 50
0
votes
1
reply
171
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 24 days ago by
Gordon Smyth
50k • written 25 days ago by
Fabian
• 0
0
votes
11
replies
586
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 23 days ago by
Gordon Smyth
50k • written 4 weeks ago by
mico
• 0
0
votes
1
reply
184
views
ExactTest vs QLFTest
edgeR
updated 26 days ago by
Gordon Smyth
50k • written 29 days ago by
fr8712ca-s
• 0
1
vote
6
replies
381
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
4 weeks ago
mico
• 0
2
votes
6
replies
335
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
5 weeks ago
tsl0026
• 0
5
votes
4
replies
330
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
5 weeks ago
pl23
• 0
0
votes
8
replies
525
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
6 weeks ago • updated 5 weeks ago
Marianna
▴ 10
3
votes
2
replies
306
views
How does one test for interactions in EdgeR?
edgeR
6 weeks ago
pl23
• 0
0
votes
4
replies
268
views
Nested paired design
edgeR
7 weeks ago
manduchi
▴ 10
1
vote
2
replies
238
views
How to get normalized values for methylation counts in edgeR
edgeR
MethylationArray
7 weeks ago
mico
• 0
2
votes
3
replies
285
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 7 weeks ago by
James W. MacDonald
65k • written 7 weeks ago by
Shaimaa Gamal
• 0
4
votes
4
replies
370
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 8 weeks ago by
James W. MacDonald
65k • written 10 weeks ago by
Geo
• 0
6
votes
7
replies
478
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
aa.machado001
• 0
1
vote
8
replies
464
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 8 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
sat
• 0
0
votes
0
replies
165
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
9 weeks ago
Jawahar
• 0
2
votes
4
replies
456
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
9 weeks ago
Sabiha
▴ 20
0
votes
3
replies
272
views
EdgeR for methylation analysis when there is no replicates
RRBSdata
edgeR
updated 9 weeks ago by
Gordon Smyth
50k • written 9 weeks ago by
annasoudi
• 0
3
votes
3
replies
578
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 9 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
Jurgen
• 0
4
votes
9
replies
1.0k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2
edgeR
11 weeks ago • updated 10 weeks ago
Luca
• 0
0
votes
1
reply
252
views
download problem
edgeR
updated 11 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
theokirkland3
• 0
0
votes
5
replies
532
views
Help with model for differential expression analysis
DifferentialExpression
edgeR
12 weeks ago • updated 8 weeks ago
Lucy
▴ 60
1
vote
2
replies
365
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
3 months ago
Sabiha
▴ 20
5
votes
2
replies
462
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
annikagable
• 0
1
vote
2
replies
321
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
Jurgen
• 0
7
votes
2
replies
623
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
annikagable
• 0
0
votes
3
replies
399
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
4 months ago • updated 3 months ago
Karthik
• 0
4
votes
2
replies
522
views
DecideTest vs topTAGs in edgeR
RNAseq
StatisticalMethod
edgeR
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
alvaroperona1
▴ 10
6
votes
7
replies
851
views
[Bug] Segfault in edgeR::cpm
edgeR
segfault
updated 5 months ago by
ATpoint
★ 4.0k • written 5 months ago by
jonas.freimuth
▴ 20
0
votes
0
replies
236
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
5 months ago
Florian
• 0
1
vote
3
replies
397
views
edgeR: Time course RNA-seq experiments
edgeR
updated 5 months ago by
ATpoint
★ 4.0k • written 5 months ago by
SuperDad
• 0
0
votes
1
reply
397
views
Batch effect adjust in model matrix
BatchEffect
edgeR
updated 6 months ago by
ATpoint
★ 4.0k • written 6 months ago by
Giuseppe
• 0
1
vote
6
replies
2.6k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma
edger
timecourse
without replicate
voom
written 7.4 years ago by
Camila Orellana
▴ 10
1
vote
4
replies
652
views
MDS plot edgeR
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
jbono
▴ 10
3
votes
3
replies
533
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression
edgeR
limma
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
stuartthafass
• 0
1
vote
2
replies
665
views
Should I use CPM or Voom transformed values for downstream analysis?
edgeR
limma
6 months ago
petertam1343
• 0
1
vote
5
replies
665
views
Why do I obtain Identical Adj.P value when running edgeR ?
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
Mohamed
▴ 30
3
votes
3
replies
501
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest
edgeR
DESeq2
6 months ago
Nisha
• 0
2
votes
3
replies
754
views
Import Salmon data with tximport and pool technical replicates
tximport
edgeR
written 7 months ago by
Vitor
• 0
1
vote
5
replies
600
views
edgeR design/contrast matrix troubles
edgeR
updated 6 months ago by
James W. MacDonald
65k • written 6 months ago by
alex.hart
• 0
0
votes
1
reply
459
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2
RNASeqData
edgeR
limma
DifferentialExpression
updated 7 months ago by
ATpoint
★ 4.0k • written 7 months ago by
Sep
• 0
50 results • Page
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Answer: New genes that did not exist in dds object suddenly showed up after degPatterns
by
Michael Love
41k
May be documented by the software you are using? https://github.com/lpantano/DEGreport
Answer: Doing comparison of RNA-seq data using Deseq2
by
Michael Love
41k
Take a look at our workflow, this starts from a beginner's level. You could export from Excel using CSV or TSV, then read into R. htt…
Answer: WGCNA: analysis of complex trait associations with regressions
by
James W. MacDonald
65k
This support site is meant to help people with questions about Bioconductor packages (WGCNA is not a Bioconductor package). You might try o…
Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Votes
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
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