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Showing :
EdgeR
•
reset
3
votes
6
replies
292
views
FilterByExpr low counts with small sample size
edgeR
5 days ago • updated 15 hours ago
Jonathan
▴ 10
3
votes
3
replies
279
views
permutation test in edgeR
rna-seq
edgeR
updated 2 days ago by
Gordon Smyth
50k • written 14 days ago by
Netanel
• 0
6
votes
10
replies
1.5k
views
Which input file is used for DGEList in EgdeR?
salmon
edgeR
tximport
nf-core
gene_counts
updated 3 days ago by
i.atanasoai
• 0 • written 14 months ago by
mohammedtoufiq91
▴ 10
0
votes
3
replies
113
views
Finding DEGs by using edgeR
subsettingdata
edgeR
designmatrix
updated 3 days ago by
Gordon Smyth
50k • written 4 days ago by
prity6459
• 0
0
votes
2
replies
79
views
How to make DGEList and design matrix by edgeR package
DGEList
edgeR
3 days ago
prity6459
• 0
0
votes
1
reply
100
views
Log-cpm values from limma
limma
edgeR
RNASeq
updated 3 days ago by
Gordon Smyth
50k • written 4 days ago by
Shaimaa Gamal
• 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2
edgeR
rna-seq
updated 4 days ago by
Elizabeth
• 0 • written 8.8 years ago by
gthm
▴ 30
1
vote
3
replies
317
views
Why is my gene not significantly differentially expressed?
limmaGUI
edgeR
limma
updated 7 days ago by
Gordon Smyth
50k • written 13 days ago by
Simran
• 0
5
votes
6
replies
391
views
Not fully paired differential gene expression analysis
edgeR
DifferentialExpression
updated 10 days ago by
ATpoint
★ 4.0k • written 13 days ago by
nhaus
▴ 30
1
vote
3
replies
227
views
Lib sizes in the DGE object are different from original lib sizes
edgeR
DifferentialExpression
updated 17 days ago by
James W. MacDonald
65k • written 17 days ago by
Shaimaa Gamal
• 0
0
votes
2
replies
144
views
edgeR analysis: glm functions and offset matrix
tximport
edgeR
Normalization
19 days ago
Marianna
▴ 20
0
votes
4
replies
388
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat
sva
edgeR
21 days ago • updated 20 days ago
Lucy
▴ 60
0
votes
5
replies
1.8k
views
EdgeR: paired samples together with independant samples
RNASeq
edgeR
RNASeq
edgeR
updated 21 days ago by
Gordon Smyth
50k • written 11.5 years ago by
Maria Keays
▴ 30
3
votes
5
replies
334
views
Differing results from plotMDS and PCAtools
edgeR
PCAtools
updated 23 days ago by
Gordon Smyth
50k • written 25 days ago by
Fabian
• 0
0
votes
2
replies
1.1k
views
library size and fold changes
edgeR
edgeR
updated 23 days ago by
Gordon Smyth
50k • written 12.4 years ago by
Bogdan
▴ 670
0
votes
6
replies
310
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata
edgeR
updated 24 days ago by
Gordon Smyth
50k • written 25 days ago by
Faisal
• 0
5
votes
3
replies
677
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR
DifferentialExpression
updated 26 days ago by
Gordon Smyth
50k • written 4 weeks ago by
Jack S.
▴ 50
0
votes
1
reply
214
views
Using splicing junction counts with edgeR/limma-voom
splicing
limma
edgeR
updated 4 weeks ago by
Gordon Smyth
50k • written 4 weeks ago by
scoops_streams_06
• 0
2
votes
3
replies
276
views
edgeR, 3 x 2 design with a batch effect and contrasts
design
edgeR
contrasts
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
JKim
• 0
2
votes
2
replies
241
views
between lane normalization upper quantile
EDASeq
edgeR
5 weeks ago
elesofi
• 0
0
votes
2
replies
254
views
RNAseq analysis
rnaseqGene
edgeR
DEGraph
DifferentialExpression
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
z_bahari
• 0
2
votes
2
replies
242
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma
fit
design
RNASeq
edgeR
5 weeks ago
Sabiha
▴ 20
0
votes
3
replies
356
views
Cross-species analysis - how to compute the mid parent value?
DESeq2
limma
edgeR
DifferentialExpression
written 11 weeks ago by
pl23
• 0
3
votes
4
replies
390
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk
edgeR
DifferentialExpression
updated 6 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Jack S.
▴ 50
0
votes
11
replies
689
views
Strange logFC values in differential methylation site anslysis
edgeR
MethylationArray
updated 7 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
mico
• 0
0
votes
1
reply
210
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks ago by
Fabian
• 0
0
votes
1
reply
232
views
ExactTest vs QLFTest
edgeR
updated 7 weeks ago by
Gordon Smyth
50k • written 7 weeks 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 14 months ago by
Rebekah
• 0
1
vote
6
replies
447
views
Library size normalization in methylation count analysis
edgeR
MethylationArray
8 weeks ago
mico
• 0
5
votes
4
replies
371
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
9 weeks ago • updated 8 weeks ago
pl23
• 0
0
votes
8
replies
599
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
10 weeks ago • updated 8 weeks ago
Marianna
▴ 20
2
votes
6
replies
388
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
9 weeks ago
tsl0026
• 0
3
votes
2
replies
377
views
How does one test for interactions in EdgeR?
edgeR
10 weeks ago • updated 9 weeks ago
pl23
• 0
1
vote
2
replies
302
views
How to get normalized values for methylation counts in edgeR
edgeR
MethylationArray
10 weeks ago
mico
• 0
0
votes
4
replies
319
views
Nested paired design
edgeR
10 weeks ago
manduchi
▴ 10
2
votes
3
replies
344
views
TMM normalization after RUVg correction
RUVSeq
limma
DifferentialExpression
edgeR
Normalization
updated 11 weeks ago by
James W. MacDonald
65k • written 11 weeks ago by
Shaimaa Gamal
• 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
1
vote
8
replies
519
views
edgeR error "Design matrix not of full rank"
edgeR
methylation
updated 12 weeks ago by
Gordon Smyth
50k • written 12 weeks ago by
sat
• 0
4
votes
4
replies
417
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 12 weeks ago by
James W. MacDonald
65k • written 3 months ago by
Geo
• 0
0
votes
5
replies
594
views
Help with model for differential expression analysis
DifferentialExpression
edgeR
3 months ago • updated 12 weeks ago
Lucy
▴ 60
6
votes
7
replies
539
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 12 weeks ago by
Gordon Smyth
50k • written 12 weeks ago by
aa.machado001
• 0
0
votes
0
replies
227
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
540
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
324
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
642
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
3 months ago
Luca
• 0
5
votes
7
replies
10.0k
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
0
votes
1
reply
291
views
download problem
edgeR
updated 3 months ago by
Gordon Smyth
50k • written 3 months ago by
theokirkland3
• 0
3
votes
1
reply
1.7k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR
RnaSeqSampleSizeData
RNAseq
updated 3 months ago by
Gordon Smyth
50k • written 3.0 years ago by
Lucy
▴ 60
1
vote
2
replies
427
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod
FoldChange
edgeR
RNASeq
4 months ago
Sabiha
▴ 20
50 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 - dispersion estimation when there is none
by
WardDeb
• 0
Thank you for the pointers, I'll revert back again to the method section of the paper. As for the negative relationship of the estimated di…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
Gayatri
• 0
Hello James, How to generate the db? By running the makeOrgPackageFromNCBI() command? I have tried doing that, first by just deleting the …
Answer: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
Tim Peters
▴ 170
Hi Jose and Russ, Apologies to Jose for not seeing this earlier. Sometimes the loess smoother in the bottom panel will throw this error …
Comment: Trying to use enrichGO
by
fernanda.backsouza
• 0
Sure, I changed it but still NULL G0 <- enrichGO( gene = ortologos_filtrados$Gene.ID, OrgDb = org.Cs.eg.db, keyType = "ENTREZID",…
Answer: limma-voom: Calculate the log-fold change in gene expression within a sample
by
Gordon Smyth
50k
No, you cannot use residuals to compute logFCs. From the information you give, I guess that you need to add individual-specific condition …
Votes
Answer: DESeq2 - dispersion estimation when there is none
Comment: Cannabis and KEGGgraph
Comment: Cannabis and KEGGgraph
Answer: Cannabis and KEGGgraph
Answer: Differentially expressed genes in monocle pseudotime
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