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edger
•
reset
1
vote
2
replies
58
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
13 hours ago • updated 41 minutes ago
JKim
• 0
0
votes
2
replies
152
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 3 days ago by
Gordon Smyth
50k • written 3 days ago by
z_bahari
• 0
2
votes
2
replies
150
views
between lane normalization upper quantile
EDASeq
edgeR
4 days ago • updated 19 hours ago
elesofi
• 0
2
votes
2
replies
139
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
5 days ago • updated 4 days ago
Sabiha
▴ 20
0
votes
3
replies
273
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 6 weeks ago by
pl23
• 0
3
votes
4
replies
251
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 12 days ago by
Gordon Smyth
50k • written 14 days ago by
Jack S.
▴ 50
0
votes
1
reply
157
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 14 days ago by
Gordon Smyth
50k • written 15 days ago by
Fabian
• 0
0
votes
11
replies
542
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 14 days ago by
Gordon Smyth
50k • written 21 days ago by
mico
• 0
0
votes
1
reply
170
views
ExactTest vs QLFTest
edgeR
updated 17 days ago by
Gordon Smyth
50k • written 19 days ago by
fr8712ca-s
• 0
1
vote
6
replies
331
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
21 days ago
mico
• 0
2
votes
6
replies
297
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
4 weeks ago • updated 28 days ago
tsl0026
• 0
5
votes
4
replies
311
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
4 weeks ago • updated 25 days ago
pl23
• 0
0
votes
8
replies
502
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
5 weeks ago • updated 27 days ago
Marianna
▴ 10
3
votes
2
replies
288
views
How does one test for interactions in EdgeR?
edgeR
5 weeks ago • updated 4 weeks ago
pl23
• 0
0
votes
4
replies
252
views
Nested paired design
edgeR
5 weeks ago
manduchi
▴ 10
1
vote
2
replies
220
views
How to get normalized values for methylation counts in edgeR
edgeR
MethylationArray
5 weeks ago
mico
• 0
2
votes
3
replies
273
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 6 weeks ago by
James W. MacDonald
65k • written 6 weeks ago by
Shaimaa Gamal
• 0
4
votes
4
replies
354
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 7 weeks ago by
James W. MacDonald
65k • written 9 weeks ago by
Geo
• 0
6
votes
7
replies
445
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
aa.machado001
• 0
1
vote
8
replies
428
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
sat
• 0
0
votes
0
replies
147
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
8 weeks ago
Jawahar
• 0
2
votes
4
replies
426
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
8 weeks ago
Sabiha
▴ 20
0
votes
3
replies
251
views
EdgeR for methylation analysis when there is no replicates
RRBSdata
edgeR
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
annasoudi
• 0
3
votes
3
replies
549
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
Jurgen
• 0
4
votes
9
replies
989
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2
edgeR
10 weeks ago • updated 8 weeks ago
Luca
• 0
0
votes
1
reply
234
views
download problem
edgeR
updated 10 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
theokirkland3
• 0
0
votes
5
replies
516
views
Help with model for differential expression analysis
DifferentialExpression
edgeR
11 weeks ago • updated 7 weeks ago
Lucy
▴ 60
1
vote
2
replies
355
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
12 weeks ago
Sabiha
▴ 20
5
votes
2
replies
436
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
302
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
575
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
385
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
3 months ago
Karthik
• 0
4
votes
2
replies
501
views
DecideTest vs topTAGs in edgeR
RNAseq
StatisticalMethod
edgeR
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
alvaroperona1
▴ 10
6
votes
7
replies
831
views
[Bug] Segfault in edgeR::cpm
edgeR
segfault
updated 4 months ago by
ATpoint
★ 3.9k • written 5 months ago by
jonas.freimuth
▴ 20
0
votes
0
replies
228
views
Dual species RNA-seq, Library size and normalization
Normalization
edgeR
RNASeq
DESeq2
5 months ago
Florian
• 0
1
vote
3
replies
390
views
edgeR: Time course RNA-seq experiments
edgeR
updated 5 months ago by
ATpoint
★ 3.9k • written 5 months ago by
SuperDad
• 0
0
votes
1
reply
385
views
Batch effect adjust in model matrix
BatchEffect
edgeR
updated 5 months ago by
ATpoint
★ 3.9k • written 5 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 7.3 years ago by
Camila Orellana
▴ 10
1
vote
4
replies
626
views
MDS plot edgeR
edgeR
updated 5 months ago by
Gordon Smyth
50k • written 6 months ago by
jbono
▴ 10
3
votes
3
replies
522
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
637
views
Should I use CPM or Voom transformed values for downstream analysis?
edgeR
limma
6 months ago
petertam1343
• 0
1
vote
5
replies
652
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
490
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest
edgeR
DESeq2
6 months ago
Nisha
• 0
2
votes
3
replies
745
views
Import Salmon data with tximport and pool technical replicates
tximport
edgeR
written 7 months ago by
Vitor
• 0
1
vote
5
replies
583
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
445
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 6 months ago by
ATpoint
★ 3.9k • written 6 months ago by
Sep
• 0
0
votes
4
replies
785
views
Handle zero effective gene length when tximport RSEM results
tximport
edgeR
updated 6 months ago by
Michael Love
41k • written 7 months ago by
hanc
• 0
0
votes
0
replies
814
views
Tutorial:
Read data file containing both counts and annotation into edgeR
rpkm
edgeR
featureCounts
6 months ago
Gordon Smyth
50k
1
vote
7
replies
2.8k
views
EdgeR glmLRT vs glmQLFTest
edgeR
DifferentialExpression
updated 6 months ago by
lucap
• 0 • written 2.9 years ago by
Marianna
▴ 10
0
votes
8
replies
1.1k
views
Question about filterByExpr function edgeR
edgeR
7 months ago
lucap
• 0
50 results • Page
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Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Comment: Unable to annotate ExpressionSet object from hugene11st chip
by
Efra
• 0
I did as you told, and after running ```eset.annot <- annotateEset(eset, hugene11sttranscriptcluster.db)``` I got the next output: ``` 'se…
Comment: BioC2024 abstract submission is open!
by
howell
• 0
What are the conditions for approval of people in difficult circumstances? I want this scholarship
Comment: European Bioconductor Conference 2023 planning
by
william
• 0
[@MariaDoyle][1] Without a doubt. In that position, I will be included in the discussion. [1]: https://support.bioconductor.org/u/239…
Comment: Problem converting msigdb Human symbols to Zebrafish in gmt format
by
Georg
• 0
Thank you for the detailed response. The code worked right away. I appreciate the quick response.
Votes
C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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