Showing : edgeR • reset
1
vote
8
replies
1.8k
views
Advice on appropriateness of an offset in glmGamPoi/edgeR
DESeq2 glmGamPoi offset edgeR scRNAseq
updated 16 months ago by 53k • written 16 months ago by • 0
3
votes
5
replies
3.3k
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 16 months ago by • 0 • written 20 months ago by ▴ 60
0
votes
4
replies
1.2k
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
17 months ago vohara4 • 0
3
votes
6
replies
1.3k
views
Comapre two groups in edgeR- Coefficient and logFC explanation
edgeR
17 months ago JG13 • 0
3
votes
2
replies
1.2k
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
18 months ago mohammedtoufiq91 ▴ 10
3
votes
3
replies
1.2k
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 18 months ago by 53k • written 18 months ago by • 0
1
vote
3
replies
1.1k
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 18 months ago by 53k • written 18 months ago by • 0
0
votes
1
reply
637
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 18 months ago by 53k • written 18 months ago by • 0
4
votes
2
replies
1.8k
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
18 months ago gene_bioconductor ▴ 10
1
vote
2
replies
1.6k
views
Citation for edgeR user guide
edgeR
written 18 months ago by ▴ 30
4
votes
6
replies
1.8k
views
FilterByExpr low counts with small sample size
edgeR
19 months ago Jonathan ▴ 10
0
votes
2
replies
704
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
19 months ago prity6459 • 0
0
votes
3
replies
970
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 19 months ago by 53k • written 19 months ago by • 0
5
votes
3
replies
1.5k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 18 months ago by 53k • written 19 months ago by • 0
3
votes
3
replies
1.8k
views
permutation test in edgeR
rna-seq edgeR
updated 19 months ago by 53k • written 19 months ago by • 0
1
vote
3
replies
949
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 19 months ago by 53k • written 19 months ago by • 0
5
votes
6
replies
1.5k
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 19 months ago by ★ 5.0k • written 19 months ago by ▴ 70
1
vote
3
replies
897
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
2
replies
916
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
19 months ago Marianna ▴ 20
0
votes
4
replies
1.5k
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
19 months ago Lucy ▴ 60
3
votes
6
replies
2.2k
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
written 19 months ago by • 0
0
votes
6
replies
1.3k
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 19 months ago by 53k • written 19 months ago by • 0
0
votes
1
reply
1.1k
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 20 months ago by 53k • written 20 months ago by • 0
8
votes
5
replies
3.2k
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 12 months ago by 53k • written 20 months ago by ▴ 60
2
votes
3
replies
1.1k
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 20 months ago by 53k • written 20 months ago by • 0
0
votes
2
replies
859
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 20 months ago by 53k • written 20 months ago by • 0
2
votes
2
replies
940
views
between lane normalization upper quantile
EDASeq edgeR
20 months ago elesofi • 0
2
votes
2
replies
837
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
20 months ago Sabiha ▴ 20
1
vote
3
replies
1.0k
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 21 months ago by • 0
0
votes
1
reply
552
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 20 months ago by 53k • written 20 months ago by • 0
0
votes
11
replies
1.9k
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 20 months ago by 53k • written 20 months ago by • 0
0
votes
1
reply
705
views
ExactTest vs QLFTest
edgeR
updated 20 months ago by 53k • written 20 months ago by • 0
1
vote
7
replies
1.7k
views
Library size normalization in methylation count analysis
edgeR MethylationArray
updated 12 months ago by • 0 • written 20 months ago by • 0
2
votes
6
replies
1.0k
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
21 months ago tsl0026 • 0
5
votes
4
replies
1.1k
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
21 months ago pl23 • 0
0
votes
8
replies
1.8k
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
21 months ago Marianna ▴ 20
5
votes
2
replies
1.8k
views
How does one test for interactions in EdgeR?
edgeR
21 months ago pl23 • 0
0
votes
4
replies
887
views
Nested paired design
edgeR
21 months ago manduchi ▴ 10
1
vote
2
replies
1.1k
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
21 months ago mico • 0
2
votes
3
replies
1.1k
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 21 months ago by 68k • written 21 months ago by • 0
4
votes
4
replies
931
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 21 months ago by 68k • written 22 months ago by • 0
6
votes
7
replies
1.2k
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 21 months ago by 53k • written 21 months ago by • 0
1
vote
8
replies
1.5k
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 21 months ago by 53k • written 21 months ago by • 0
0
votes
0
replies
928
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
22 months ago Jawahar • 0
2
votes
4
replies
2.2k
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
22 months ago Sabiha ▴ 20
0
votes
3
replies
1.3k
views
EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 22 months ago by 53k • written 22 months ago by • 0
3
votes
3
replies
1.9k
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 22 months ago by 53k • written 22 months ago by • 0
4
votes
9
replies
2.4k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
22 months ago Luca • 0
0
votes
1
reply
619
views
download problem
edgeR
updated 22 months ago by 53k • written 22 months ago by • 0
0
votes
5
replies
1.4k
views
Help with model for differential expression analysis
DifferentialExpression edgeR
22 months ago • updated 21 months ago Lucy ▴ 60
2,031 results • Page 2 of 41
Recent ...
Replies
Answer: Post translational modifications and phosphoproteomics in limpa? by Gordon Smyth 53k
Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Matthew Thornton ▴ 380
WOW! Thank you so much for the information. I will do this.
Comment: "Watched Tags" are being erased rather than updated by RalphSavage99 • 0
Thanks for sharing https://github.com/Bioconductor/support.bioconductor.org/issues/112
Answer: Add additional maintainer for MOFA2 by shepherl 4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Awards • All
Popular Question to Hervé Pagès 16k
Popular Question to shepherl 4.2k
Scholar to James W. MacDonald 68k
Popular Question to Daniel Cameron ▴ 40
Popular Question to Peter Hickey ▴ 760
Locations • All
Vietnam, 1 minute ago
United States, 40 minutes ago
Germany, 1 hour ago
United States, 1 hour ago
United States, 1 hour ago
Traffic: 766 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