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Showing :
edger
•
reset
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
7
replies
2.8k
views
EdgeR glmLRT vs glmQLFTest
edgeR
DifferentialExpression
updated 7 months ago by
lucap
• 0 • written 2.9 years ago by
Marianna
▴ 10
2
votes
3
replies
755
views
Import Salmon data with tximport and pool technical replicates
tximport
edgeR
written 7 months ago by
Vitor
• 0
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
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
2
votes
5
replies
1.3k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R
edgeR
RNASeq
8 months ago
mohammedtoufiq91
▴ 10
4
votes
9
replies
1.1k
views
RNA seq differential expression analysis for large sample size
edgeR
DESeq2
8 months ago
Luca
• 0
0
votes
4
replies
796
views
Handle zero effective gene length when tximport RSEM results
tximport
edgeR
updated 7 months ago by
Michael Love
41k • written 7 months ago by
hanc
• 0
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
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
3
votes
2
replies
16k
views
how to calculate gene length to be used in rpkm() in edgeR
RNASeq
edgeR
rpkm
updated 11 months ago by
Gordon Smyth
50k • written 9.9 years ago by
shirley zhang
★ 1.0k
0
votes
9
replies
802
views
estimateDisp() error
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
ASNbioinf
• 0
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
5
votes
9
replies
2.4k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger
calcnormfactors
updated 7 months ago by
Novice_cam
• 0 • written 6.4 years ago by
knaxerova
▴ 10
1
vote
5
replies
602
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
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
0
votes
2
replies
427
views
EdgeR FTest
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
nawaz.u.toyama
• 0
1
vote
4
replies
654
views
MDS plot edgeR
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 6 months ago by
jbono
▴ 10
4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 6 months ago by
Gordon Smyth
50k • written 21 months ago by
Mohamed
▴ 30
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
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
2
votes
8
replies
2.1k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
11 months ago • updated 10 months ago
Luis
• 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
1
vote
5
replies
768
views
Recommendation for large.n in filterByExpr
scRNAseq
edgeR
SingleCellExperiment
7 months ago
duez.tolga
• 0
3
votes
3
replies
502
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest
edgeR
DESeq2
6 months ago
Nisha
• 0
1
vote
1
reply
379
views
A query about selecting the coefficient in glmLRT to test for by index
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
S
• 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
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
2
votes
1
reply
599
views
edgeR with Successive Differences Contrast Coding?
hypothesisTesting
contrastCoding
edger
ExperimentalDesign
expressionDifferences
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
Hannes
• 0
0
votes
3
replies
1.2k
views
EdgeR glm based analysis
edgeR
edgeR
10.2 years ago • updated 7 months ago
Gordon Smyth
50k
1
vote
1
reply
507
views
Using R to measure differential gene expression of one gene due to different treatments using RNASeq counts
DESeq2
edgeR
RNAseq
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
cmareevicars
• 0
1
vote
5
replies
667
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
0
votes
1
reply
378
views
Differential express genes in one group across all time points
DESeq2
edgeR
BP4RNAseq
ensemblVEP
updated 11 months ago by
Michael Love
41k • written 11 months ago by
DHARMESH
• 0
0
votes
1
reply
460
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
0
votes
2
replies
821
views
catchSalmon
catchSalmon
edgeR
updated 11 months ago by
Gordon Smyth
50k • written 2.6 years ago by
Ina Hoeschele
▴ 620
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
0
votes
11
replies
2.6k
views
edgeR contrasts
edgeR
updated 7 months ago by
James W. MacDonald
65k • written 18 months ago by
ignadb
• 0
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
6
replies
336
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
5 weeks ago
tsl0026
• 0
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
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
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
3
votes
9
replies
1.6k
views
Question about filter by expression (filterByExpr) in edgeR
CPM
filterByExpr
edgeR
design
model.matrix
12 months ago
mohammedtoufiq91
▴ 10
0
votes
1
reply
587
views
Subtype specific differential expression analysis
R
limmaGUI
edgeR
limma
regutools
updated 11 months ago by
Gordon Smyth
50k • written 11 months ago by
qiz218591
• 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
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
5
votes
4
replies
332
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
5 weeks ago
pl23
• 0
2
votes
1
reply
580
views
DESeq2 or edgeR for Presence and Absence of Proteins
edgeR
DESeq2
updated 10 months ago by
ATpoint
★ 4.0k • written 10 months ago by
calvincornell1996
• 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
5
votes
7
replies
1.7k
views
Problem with installing packages made by makeOrgPackageFromNCBI
AnnotationForge
makeOrgPackageFromNCBI
gene ontology
edgeR
pathwayanalysis
updated 11 months ago by
L
▴ 50 • written 4.1 years ago by
babak.loghmani
▴ 20
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
by
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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