Showing : edger • reset
2
votes
2
replies
57
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
16 hours ago • updated 2 hours ago mohammedtoufiq91 ▴ 10
2
votes
3
replies
158
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 6 days ago by 50k • written 6 days ago by • 0
1
vote
3
replies
267
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 7 days ago by 50k • written 8 days ago by • 0
0
votes
1
reply
181
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 19 days ago by 50k • written 19 days ago by • 0
4
votes
2
replies
644
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
19 days ago • updated 15 days ago gene_bioconductor ▴ 10
1
vote
2
replies
212
views
Citation for edgeR user guide
edgeR
written 28 days ago by ▴ 30
4
votes
6
replies
480
views
FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 29 days ago Jonathan ▴ 10
0
votes
2
replies
153
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
4 weeks ago prity6459 • 0
0
votes
3
replies
219
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
5
votes
3
replies
323
views
Log-cpm values from limma
limma edgeR RNASeq
updated 11 days ago by 50k • written 4 weeks ago by • 0
3
votes
3
replies
371
views
permutation test in edgeR
rna-seq edgeR
updated 4 weeks ago by 50k • written 6 weeks ago by • 0
1
vote
3
replies
371
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
5
votes
6
replies
464
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 5 weeks ago by ★ 4.1k • written 6 weeks ago by ▴ 30
1
vote
3
replies
285
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 6 weeks ago by 66k • written 6 weeks ago by • 0
0
votes
2
replies
201
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
6 weeks ago Marianna ▴ 20
0
votes
4
replies
450
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
7 weeks ago Lucy ▴ 60
3
votes
5
replies
419
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
0
votes
6
replies
378
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
0
votes
1
reply
257
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
5
votes
3
replies
749
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 7 weeks ago by 50k • written 8 weeks ago by ▴ 50
2
votes
3
replies
317
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
0
votes
2
replies
307
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
2
votes
2
replies
278
views
between lane normalization upper quantile
EDASeq edgeR
9 weeks ago elesofi • 0
2
votes
2
replies
292
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 weeks ago Sabiha ▴ 20
1
vote
3
replies
446
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
3
votes
4
replies
536
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 10 weeks ago by 50k • written 11 weeks ago by ▴ 50
0
votes
1
reply
244
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
0
votes
11
replies
802
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 11 weeks ago by 50k • written 12 weeks ago by • 0
0
votes
1
reply
294
views
ExactTest vs QLFTest
edgeR
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
1
vote
6
replies
532
views
Library size normalization in methylation count analysis
edgeR MethylationArray
12 weeks ago mico • 0
2
votes
6
replies
446
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
3 months ago tsl0026 • 0
5
votes
4
replies
437
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
3 months ago • updated 12 weeks ago pl23 • 0
0
votes
8
replies
692
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
3 months ago Marianna ▴ 20
3
votes
2
replies
511
views
How does one test for interactions in EdgeR?
edgeR
3 months ago pl23 • 0
0
votes
4
replies
370
views
Nested paired design
edgeR
3 months ago manduchi ▴ 10
1
vote
2
replies
356
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
3 months ago mico • 0
2
votes
3
replies
395
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 66k • written 3 months ago by • 0
4
votes
4
replies
465
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by 66k • written 4 months ago by • 0
6
votes
7
replies
617
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
1
vote
8
replies
586
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 3 months ago by 50k • written 3 months ago by • 0
0
votes
0
replies
272
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
4 months ago Jawahar • 0
2
votes
4
replies
655
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago Sabiha ▴ 20
0
votes
3
replies
394
views
EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
3
votes
3
replies
733
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
4 months ago Luca • 0
0
votes
1
reply
328
views
download problem
edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
0
votes
5
replies
650
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
1
vote
2
replies
500
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
5 months ago Sabiha ▴ 20
5
votes
2
replies
610
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 5 months ago by 50k • written 5 months ago by • 0
1
vote
2
replies
469
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: slingshot: error with plot3d.SlingshotDataSet by Happiness • 0
Hi please i am encountering similar issue how did you fix it. Here is the code: ## Run Slingshot p3.neuron.sds <- slingshot(Embeddings(…
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data by mohammedtoufiq91 ▴ 10
https://support.bioconductor.org/u/5106/ thank you very much.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Thank you so much!
Answer: recount3 problem downloading data from source sra by Leonardo Collado Torres ★ 1.0k
Hi, I wasn't able to reproduce the issue on both bioc 3.19 (current release version) and 3.18 (closer to your session info). My guess is…
Answer: Running ENmix with mouse methylation manifest: readidat error - Error in readman by minardsmitha ▴ 10
Well it turns out there is a typo in the manifest file name. This particular issue is resolved by correcting the typo. A new error now …
Votes
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
Comment: Ensembl plants at annotationHub?
how to control age and gender effect in expression data using DESeq2
Answer: Error retrieving ensembl gene id using biomaRt...
Awards • All
Scholar to Mike Smith ★ 6.5k
Popular Question to mohammedtoufiq91 ▴ 10
Popular Question to Gordon Smyth 50k
Popular Question to bas_work ▴ 30
Popular Question to landenshanie ▴ 40
Locations • All
India, 2 minutes ago
WEHI, Melbourne, Australia, 7 minutes ago
Slovakia, 14 minutes ago
Vietnam, 43 minutes ago
Hong Kong, 1 hour ago
Traffic: 516 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