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edger
•
reset
9
votes
12
replies
7.7k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 9 hours ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
4
votes
12
replies
3.7k
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
11
replies
668
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
mico
• 0
0
votes
11
replies
2.7k
views
edgeR contrasts
edgeR
updated 8 months ago by
James W. MacDonald
65k • written 19 months ago by
ignadb
• 0
5
votes
11
replies
2.9k
views
Visualization of negative log CPM values
Visualization
Normalization
ggplot2
edgeR
written 10 months ago by
Sabiha
▴ 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 8 months ago by
Novice_cam
• 0 • written 6.4 years ago by
knaxerova
▴ 10
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2
edgeR
3 months ago
Luca
• 0
0
votes
9
replies
832
views
estimateDisp() error
edgeR
updated 8 months ago by
Gordon Smyth
50k • written 8 months ago by
ASNbioinf
• 0
4
votes
9
replies
1.2k
views
RNA seq differential expression analysis for large sample size
edgeR
DESeq2
8 months ago
Luca
• 0
2
votes
8
replies
2.2k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
12 months ago • updated 10 months ago
Luis
• 0
0
votes
8
replies
1.2k
views
Question about filterByExpr function edgeR
edgeR
8 months ago
lucap
• 0
1
vote
8
replies
508
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 11 weeks ago by
Gordon Smyth
50k • written 12 weeks ago by
sat
• 0
0
votes
8
replies
589
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
9 weeks ago • updated 8 weeks ago
Marianna
▴ 20
6
votes
8
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 5 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
6
votes
7
replies
902
views
[Bug] Segfault in edgeR::cpm
edgeR
segfault
updated 5 months ago by
ATpoint
★ 4.0k • written 6 months ago by
jonas.freimuth
▴ 20
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering
RNA-Seq
CPM
edgeR
filterByExpr
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
mohammedtoufiq91
▴ 10
4
votes
7
replies
13k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq
R
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 21 months ago by
Mohamed
▴ 30
6
votes
7
replies
529
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 11 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
aa.machado001
• 0
2
votes
7
replies
2.9k
views
EdgeR glmLRT vs glmQLFTest
edgeR
DifferentialExpression
updated 7 months ago by
lucap
• 0 • written 3.0 years ago by
Marianna
▴ 20
5
votes
7
replies
9.9k
views
threshold to filter lowly expressed genes
edger
rnaseq
updated 3 months ago by
Shaimaa Gamal
• 0 • written 7.1 years ago by
myprogramming2016
• 0
5
votes
6
replies
373
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 5 days ago by
ATpoint
★ 4.0k • written 9 days ago by
nhaus
▴ 30
0
votes
6
replies
301
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 20 days ago by
Gordon Smyth
50k • written 21 days ago by
Faisal
• 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
2
votes
6
replies
379
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
8 weeks ago
tsl0026
• 0
3
votes
6
replies
813
views
Question on constructing design matrix and defining contrasts for analysis
wgcna
DESeq2
edgeR
limma
design
updated 10 months ago by
Gordon Smyth
50k • written 10 months ago by
mohammedtoufiq91
▴ 10
1
vote
6
replies
430
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
7 weeks ago
mico
• 0
1
vote
5
replies
711
views
Why do I obtain Identical Adj.P value when running edgeR ?
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
Mohamed
▴ 30
3
votes
5
replies
324
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 18 days ago by
Gordon Smyth
50k • written 21 days ago by
Fabian
• 0
1
vote
5
replies
647
views
edgeR design/contrast matrix troubles
edgeR
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
alex.hart
• 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
5
replies
822
views
Recommendation for large.n in filterByExpr
scRNAseq
edgeR
SingleCellExperiment
8 months ago
duez.tolga
• 0
0
votes
5
replies
768
views
Model and Contrasts with 4 variables
contrast
edgeR
DESeq2
updated 10 months ago by
James W. MacDonald
65k • written 10 months ago by
Cristina
• 0
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
9 months ago • updated 8 months ago
mohammedtoufiq91
▴ 10
0
votes
5
replies
1.8k
views
EdgeR: paired samples together with independant samples
RNASeq
edgeR
RNASeq
edgeR
updated 16 days ago by
Gordon Smyth
50k • written 11.5 years ago by
Maria Keays
▴ 30
0
votes
5
replies
585
views
Help with model for differential expression analysis
DifferentialExpression
edgeR
3 months ago • updated 11 weeks ago
Lucy
▴ 60
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 8.2 years ago by
Radek
▴ 90
0
votes
4
replies
840
views
Handle zero effective gene length when tximport RSEM results
tximport
edgeR
updated 7 months ago by
Michael Love
41k • written 8 months ago by
hanc
• 0
3
votes
4
replies
8.5k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 11 weeks ago by
Dimitris
• 0 • written 10.8 years ago by
Makis Motakis
▴ 30
0
votes
4
replies
316
views
Nested paired design
edgeR
10 weeks ago
manduchi
▴ 10
1
vote
4
replies
696
views
MDS plot edgeR
edgeR
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
jbono
▴ 10
5
votes
4
replies
361
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
8 weeks ago
pl23
• 0
2
votes
4
replies
519
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
12 weeks ago
Sabiha
▴ 20
3
votes
4
replies
369
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Jack S.
▴ 50
3
votes
4
replies
691
views
Anova table edgeR limma
limma
RNASeq
edgeR
11 months ago
KATHERINE CHUERE NUNES
• 0
4
votes
4
replies
410
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 11 weeks ago by
James W. MacDonald
65k • written 3 months ago by
Geo
• 0
0
votes
4
replies
383
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
17 days ago • updated 16 days ago
Lucy
▴ 60
0
votes
3
replies
351
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 11 weeks ago by
pl23
• 0
0
votes
3
replies
428
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
4 months ago
Karthik
• 0
3
votes
3
replies
555
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression
edgeR
limma
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
stuartthafass
• 0
4
votes
3
replies
1.7k
views
catchSalmon for tx-level DE
catchSalmon
edgeR
updated 5 months ago by
Gordon Smyth
50k • written 3.5 years ago by
ATpoint
★ 4.0k
50 results • Page
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I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question
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Thanks Peter!
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Thank you!
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They are reorder in the decreasing order.
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