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edgeR
•
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0
votes
2
replies
72
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression
TimeCourse
timeOmics
edgeR
RNAseq
19 hours ago • updated 2 hours ago
Ashley
• 0
0
votes
1
reply
162
views
NEED FOR NESSASORY HELP
RNASeqData
edgeR
updated 11 days ago by
Gordon Smyth
50k • written 11 days ago by
z_bahari
• 0
4
votes
2
replies
603
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea
edgeR
11 days ago • updated 8 days ago
gene_bioconductor
▴ 10
1
vote
1
reply
190
views
Citation for edgeR user guide
edgeR
updated 20 days ago by
Gordon Smyth
50k • written 20 days ago by
k___
▴ 30
4
votes
6
replies
454
views
FilterByExpr low counts with small sample size
edgeR
27 days ago • updated 22 days ago
Jonathan
▴ 10
0
votes
2
replies
143
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
25 days ago
prity6459
• 0
0
votes
3
replies
204
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 25 days ago by
Gordon Smyth
50k • written 26 days ago by
prity6459
• 0
5
votes
3
replies
293
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 4 days ago by
Gordon Smyth
50k • written 26 days ago by
Shaimaa Gamal
• 0
3
votes
3
replies
360
views
permutation test in edgeR
rna-seq
edgeR
updated 23 days ago by
Gordon Smyth
50k • written 5 weeks ago by
Netanel
• 0
1
vote
3
replies
361
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 29 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Simran
• 0
5
votes
6
replies
446
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 4 weeks ago by
ATpoint
★ 4.1k • written 5 weeks ago by
nhaus
▴ 30
1
vote
3
replies
274
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 5 weeks ago by
James W. MacDonald
65k • written 5 weeks ago by
Shaimaa Gamal
• 0
0
votes
2
replies
187
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
5 weeks ago
Marianna
▴ 20
0
votes
4
replies
442
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
6 weeks ago
Lucy
▴ 60
3
votes
5
replies
404
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Fabian
• 0
0
votes
6
replies
366
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 6 weeks ago by
Gordon Smyth
50k • written 6 weeks ago by
Faisal
• 0
0
votes
1
reply
246
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
scoops_streams_06
• 0
5
votes
3
replies
728
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Jack S.
▴ 50
2
votes
3
replies
302
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
JKim
• 0
0
votes
2
replies
298
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
z_bahari
• 0
2
votes
2
replies
267
views
between lane normalization upper quantile
EDASeq
edgeR
8 weeks ago
elesofi
• 0
2
votes
2
replies
277
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
8 weeks ago
Sabiha
▴ 20
1
vote
3
replies
432
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 3 months ago by
pl23
• 0
3
votes
4
replies
473
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 9 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
Jack S.
▴ 50
0
votes
1
reply
231
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 10 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
Fabian
• 0
0
votes
11
replies
763
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 10 weeks ago by
Gordon Smyth
50k • written 11 weeks ago by
mico
• 0
0
votes
1
reply
272
views
ExactTest vs QLFTest
edgeR
updated 10 weeks ago by
Gordon Smyth
50k • written 10 weeks ago by
fr8712ca-s
• 0
1
vote
6
replies
517
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
11 weeks ago
mico
• 0
2
votes
6
replies
431
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
12 weeks ago
tsl0026
• 0
5
votes
4
replies
417
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
12 weeks ago • updated 11 weeks ago
pl23
• 0
0
votes
8
replies
672
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
3 months ago • updated 12 weeks ago
Marianna
▴ 20
3
votes
2
replies
482
views
How does one test for interactions in EdgeR?
edgeR
3 months ago
pl23
• 0
0
votes
4
replies
361
views
Nested paired design
edgeR
3 months ago
manduchi
▴ 10
1
vote
2
replies
337
views
How to get normalized values for methylation counts in edgeR
edgeR
MethylationArray
3 months ago
mico
• 0
2
votes
3
replies
382
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 3 months ago by
James W. MacDonald
65k • written 3 months ago by
Shaimaa Gamal
• 0
4
votes
4
replies
448
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by
James W. MacDonald
65k • written 4 months ago by
Geo
• 0
6
votes
7
replies
590
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
aa.machado001
• 0
1
vote
8
replies
561
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
sat
• 0
0
votes
0
replies
257
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind
edgeR
ATACSeq
DESeq2
3 months ago
Jawahar
• 0
2
votes
4
replies
625
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization
edgeR
RNASeq
3 months ago
Sabiha
▴ 20
0
votes
3
replies
356
views
EdgeR for methylation analysis when there is no replicates
RRBSdata
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
annasoudi
• 0
3
votes
3
replies
696
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
Jurgen
• 0
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2
edgeR
4 months ago • updated 3 months ago
Luca
• 0
0
votes
1
reply
317
views
download problem
edgeR
updated 4 months ago by
Gordon Smyth
50k • written 4 months ago by
theokirkland3
• 0
0
votes
5
replies
635
views
Help with model for differential expression analysis
DifferentialExpression
edgeR
4 months ago • updated 3 months ago
Lucy
▴ 60
1
vote
2
replies
485
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
4 months ago
Sabiha
▴ 20
5
votes
2
replies
590
views
Filter genes by expression for voomLmFit
DEG
edgeR
limma
voom
filterByExpr
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
1
vote
2
replies
446
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression
edgeR
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
Jurgen
• 0
7
votes
2
replies
842
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR
limma
voom
RNASeq
muscat
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
annikagable
• 0
0
votes
3
replies
472
views
'Subtracting' counts on basis of Negative control media and water samples
limma
edgeR
RNASeq
DESeq2
5 months ago
Karthik
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Can I trust the differential expression analysis when the two groups overlap on
by
Michael Love
42k
I'm wondering about sample table mixup. How have you merged your sequencing data with the phenotype data (`colData`)?
Comment: Can I trust the differential expression analysis when the two groups overlap on
by
Eric Katagirya
• 0
Thanks @mikelove , Using vst or rlog doesn't improve the segregation nor is there a remarkable difference when I use 1000 or 2000 most vari…
Answer: Batch effect correction: methylome data
by
zhouwanding
▴ 10
I agree that the batch variable should be better modeled as a co-variate than explicit batch correction. There is also RUVm (https://www.nc…
Comment: Can I trust the differential expression analysis when the two groups overlap on
by
Eric Katagirya
• 0
Thanks @bioinfguru - I did the 3-D PCA plot ![PC1 vs PC3 plot][1] and also the scree plot ![Scree plot][2] but couldn't make much of the…
Answer: Can log2cpm be used for proteomics data normalization?
by
James W. MacDonald
65k
The term 'logCPM' is short for log counts/million counts, which is generally only applicable for count-based applications like RNA-Seq. Usu…
Votes
Ensembl 112 has been released.
A: Diffbind results - non uniform width
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Answer: Error EPICv2 ChAMP
Comment: Store output of matchPWM()
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