Showing : EdgeR • reset
0
votes
4
replies
198
views
FilterByExpr low counts with small sample size
edgeR
2 days ago • updated 22 hours ago Jonathan ▴ 10
0
votes
2
replies
59
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
1 day ago prity6459 • 0
0
votes
3
replies
81
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 1 day ago by 50k • written 1 day ago by • 0
0
votes
1
reply
72
views
Log-cpm values from limma
limma edgeR RNASeq
updated 1 day ago by 50k • written 2 days ago by • 0
3
votes
3
replies
267
views
permutation test in edgeR
rna-seq edgeR
updated 5 days ago by 50k • written 12 days ago by • 0
1
vote
3
replies
311
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 5 days ago by 50k • written 10 days ago by • 0
5
votes
6
replies
384
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 7 days ago by ★ 4.0k • written 10 days ago by ▴ 30
1
vote
3
replies
223
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 14 days ago by 65k • written 14 days ago by • 0
0
votes
2
replies
142
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
17 days ago Marianna ▴ 20
0
votes
4
replies
387
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
19 days ago • updated 17 days ago Lucy ▴ 60
3
votes
5
replies
327
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 20 days ago by 50k • written 22 days ago by • 0
0
votes
6
replies
305
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 21 days ago by 50k • written 22 days ago by • 0
0
votes
1
reply
208
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 29 days ago by 50k • written 29 days ago by • 0
5
votes
3
replies
670
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 23 days ago by 50k • written 4 weeks ago by ▴ 50
2
votes
3
replies
273
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
0
votes
2
replies
251
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
2
votes
2
replies
238
views
between lane normalization upper quantile
EDASeq edgeR
5 weeks ago • updated 4 weeks ago elesofi • 0
2
votes
2
replies
239
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
354
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 11 weeks ago by • 0
3
votes
4
replies
378
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 6 weeks ago by 50k • written 6 weeks ago by ▴ 50
0
votes
1
reply
207
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
votes
11
replies
677
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 6 weeks ago by 50k • written 7 weeks ago by • 0
0
votes
1
reply
231
views
ExactTest vs QLFTest
edgeR
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
1
vote
6
replies
443
views
Library size normalization in methylation count analysis
edgeR MethylationArray
7 weeks ago mico • 0
2
votes
6
replies
383
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
9 weeks ago • updated 8 weeks ago tsl0026 • 0
5
votes
4
replies
366
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
9 weeks ago • updated 8 weeks ago pl23 • 0
0
votes
8
replies
594
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
9 weeks ago • updated 8 weeks ago Marianna ▴ 20
3
votes
2
replies
369
views
How does one test for interactions in EdgeR?
edgeR
10 weeks ago • updated 9 weeks ago pl23 • 0
0
votes
4
replies
318
views
Nested paired design
edgeR
10 weeks ago manduchi ▴ 10
1
vote
2
replies
298
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
10 weeks ago mico • 0
2
votes
3
replies
337
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 10 weeks ago by 65k • written 10 weeks ago by • 0
4
votes
4
replies
414
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 11 weeks ago by 65k • written 3 months ago by • 0
6
votes
7
replies
535
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 11 weeks ago by 50k • written 12 weeks ago by • 0
1
vote
8
replies
513
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 11 weeks ago by 50k • written 12 weeks ago by • 0
0
votes
0
replies
223
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
12 weeks ago Jawahar • 0
2
votes
4
replies
526
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago • updated 12 weeks ago Sabiha ▴ 20
0
votes
3
replies
316
views
EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
3
votes
3
replies
635
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
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
1
reply
289
views
download problem
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
0
votes
5
replies
590
views
Help with model for differential expression analysis
DifferentialExpression edgeR
3 months ago • updated 11 weeks ago Lucy ▴ 60
1
vote
2
replies
422
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
5
votes
2
replies
513
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 months ago by 50k • written 4 months ago by • 0
1
vote
2
replies
375
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
7
votes
2
replies
738
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 4 months ago by 50k • written 4 months ago by • 0
0
votes
3
replies
433
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago • updated 4 months ago Karthik • 0
4
votes
2
replies
572
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 5 months ago by 50k • written 5 months ago by ▴ 10
6
votes
7
replies
909
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 6 months ago by ★ 4.0k • written 6 months ago by ▴ 20
0
votes
0
replies
259
views
Dual species RNA-seq, Library size and normalization
Normalization edgeR RNASeq DESeq2
6 months ago Florian • 0
1
vote
3
replies
431
views
edgeR: Time course RNA-seq experiments
edgeR
updated 6 months ago by ★ 4.0k • written 6 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Thanks Robert!
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Votes
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
Awards • All
Scholar to Robert Castelo ★ 3.2k
Popular Question to James W. MacDonald 65k
Popular Question to shepherl 3.8k
Popular Question to BioinfGuru ▴ 30
Popular Question to Gordon Smyth 50k
Locations • All
United States, 2 minutes ago
France, 9 minutes ago
India, 47 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
Ireland, 1 hour ago
Traffic: 460 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6