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0
votes
0
replies
37
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
12 hours ago
Fabian
• 0
0
votes
1
reply
50
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
13 hours ago • updated 12 hours ago
Faisal
• 0
4
votes
3
replies
480
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 1 day ago by
Gordon Smyth
50k • written 8 days ago by
Jack S.
▴ 50
0
votes
1
reply
151
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 7 days ago by
Gordon Smyth
50k • written 7 days ago by
scoops_streams_06
• 0
2
votes
3
replies
220
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 10 days ago by
Gordon Smyth
50k • written 10 days ago by
JKim
• 0
2
votes
2
replies
200
views
between lane normalization upper quantile
EDASeq
edgeR
14 days ago • updated 11 days ago
elesofi
• 0
0
votes
2
replies
214
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 13 days ago by
Gordon Smyth
50k • written 14 days ago by
z_bahari
• 0
2
votes
2
replies
191
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
15 days ago • updated 14 days ago
Sabiha
▴ 20
0
votes
3
replies
307
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
289
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 23 days ago by
Gordon Smyth
50k • written 24 days ago by
Jack S.
▴ 50
0
votes
11
replies
587
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 24 days ago by
Gordon Smyth
50k • written 4 weeks ago by
mico
• 0
0
votes
1
reply
173
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 25 days ago by
Gordon Smyth
50k • written 25 days ago by
Fabian
• 0
0
votes
1
reply
186
views
ExactTest vs QLFTest
edgeR
updated 27 days ago by
Gordon Smyth
50k • written 29 days ago by
fr8712ca-s
• 0
2
votes
5
replies
1.3k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR
RNASeq
RNASeqData
Bioconductor
written 13 months ago by
Rebekah
• 0
1
vote
6
replies
382
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
4 weeks ago
mico
• 0
5
votes
4
replies
332
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
5 weeks ago
pl23
• 0
0
votes
8
replies
526
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
6 weeks ago • updated 5 weeks ago
Marianna
▴ 10
2
votes
6
replies
336
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
5 weeks ago
tsl0026
• 0
3
votes
2
replies
308
views
How does one test for interactions in EdgeR?
edgeR
6 weeks ago
pl23
• 0
1
vote
2
replies
240
views
How to get normalized values for methylation counts in edgeR
edgeR
MethylationArray
7 weeks ago
mico
• 0
0
votes
4
replies
269
views
Nested paired design
edgeR
7 weeks ago
manduchi
▴ 10
2
votes
3
replies
287
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
3
votes
4
replies
8.4k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 8 weeks ago by
Dimitris
• 0 • written 10.8 years ago by
Makis Motakis
▴ 30
1
vote
8
replies
466
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
4
votes
4
replies
371
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
0
votes
5
replies
533
views
Help with model for differential expression analysis
DifferentialExpression
edgeR
12 weeks ago • updated 8 weeks ago
Lucy
▴ 60
6
votes
7
replies
479
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
0
votes
0
replies
166
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
458
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
276
views
EdgeR for methylation analysis when there is no replicates
RRBSdata
edgeR
updated 9 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
annasoudi
• 0
3
votes
3
replies
582
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 10 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
5
votes
7
replies
9.9k
views
threshold to filter lowly expressed genes
edger
rnaseq
updated 10 weeks ago by
Shaimaa Gamal
• 0 • written 7.0 years ago by
myprogramming2016
• 0
0
votes
1
reply
253
views
download problem
edgeR
updated 11 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
theokirkland3
• 0
3
votes
1
reply
1.6k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR
RnaSeqSampleSizeData
RNAseq
updated 12 weeks ago by
Gordon Smyth
50k • written 2.9 years ago by
Lucy
▴ 60
1
vote
2
replies
367
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
3 months ago
Sabiha
▴ 20
0
votes
1
reply
1.4k
views
EdgeR norm.factor input
Normalization
edgeR
Normalization
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 10.1 years ago by
Guest User
★ 13k
5
votes
2
replies
463
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
322
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
625
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
402
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
9
votes
5
replies
5.0k
views
Differential expression analysis: Permutation Test
deseq2
limma
edger
permutation
updated 4 months ago by
Gordon Smyth
50k • written 8.1 years ago by
Radek
▴ 90
4
votes
3
replies
1.7k
views
catchSalmon for tx-level DE
catchSalmon
edgeR
updated 4 months ago by
Gordon Smyth
50k • written 3.4 years ago by
ATpoint
★ 4.0k
4
votes
2
replies
523
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
852
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
237
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
5 months ago
Florian
• 0
1
vote
3
replies
399
views
edgeR: Time course RNA-seq experiments
edgeR
updated 5 months ago by
ATpoint
★ 4.0k • written 5 months ago by
SuperDad
• 0
4
votes
12
replies
3.6k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR
SpikeIn
RNASeq
updated 6 months ago by
Miguel
• 0 • written 3.1 years ago by
robert.chen
• 0
0
votes
1
reply
399
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
50 results • Page
1 of 1
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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
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James W. MacDonald
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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
transcript name mapping between human and mouse
transcript name mapping between human and mouse
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
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