Showing : EdgeR • reset
0
votes
1
reply
164
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 20 hours ago by 50k • written 1 day ago by ▴ 10
0
votes
1
reply
74
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 1 day ago by 50k • written 1 day ago by • 0
1
vote
1
reply
165
views
Citation for edgeR user guide
edgeR
updated 10 days ago by 50k • written 10 days ago by ▴ 30
4
votes
6
replies
411
views
FilterByExpr low counts with small sample size
edgeR
16 days ago • updated 11 days ago Jonathan ▴ 10
3
votes
3
replies
326
views
permutation test in edgeR
rna-seq edgeR
updated 12 days ago by 50k • written 25 days ago by • 0
6
votes
10
replies
1.6k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 14 days ago by • 0 • written 15 months ago by ▴ 10
0
votes
3
replies
180
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 14 days ago by 50k • written 15 days ago by • 0
0
votes
2
replies
127
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
14 days ago prity6459 • 0
3
votes
1
reply
165
views
Log-cpm values from limma
limma edgeR RNASeq
updated 14 days ago by 50k • written 15 days ago by • 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 15 days ago by • 0 • written 8.8 years ago by ▴ 30
1
vote
3
replies
344
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 18 days ago by 50k • written 23 days ago by • 0
5
votes
6
replies
418
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 20 days ago by ★ 4.1k • written 24 days ago by ▴ 30
1
vote
3
replies
244
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 28 days ago by 65k • written 28 days ago by • 0
0
votes
2
replies
164
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
4 weeks ago Marianna ▴ 20
0
votes
4
replies
417
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
4 weeks ago Lucy ▴ 60
0
votes
5
replies
1.8k
views
EdgeR: paired samples together with independant samples
RNASeq edgeR RNASeq edgeR
updated 4 weeks ago by 50k • written 11.5 years ago by ▴ 30
3
votes
5
replies
373
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
0
votes
2
replies
1.1k
views
library size and fold changes
edgeR edgeR
updated 4 weeks ago by 50k • written 12.4 years ago by ▴ 670
0
votes
6
replies
352
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
5
votes
3
replies
709
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 5 weeks ago by 50k • written 6 weeks ago by ▴ 50
0
votes
1
reply
233
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
2
votes
3
replies
292
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
2
votes
2
replies
256
views
between lane normalization upper quantile
EDASeq edgeR
7 weeks ago • updated 6 weeks ago elesofi • 0
0
votes
2
replies
281
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 6 weeks ago by 50k • written 7 weeks ago by • 0
2
votes
2
replies
259
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
7 weeks ago Sabiha ▴ 20
1
vote
3
replies
402
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
422
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 8 weeks ago by 50k • written 8 weeks ago by ▴ 50
0
votes
11
replies
735
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 8 weeks ago by 50k • written 9 weeks ago by • 0
0
votes
1
reply
219
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
0
votes
1
reply
250
views
ExactTest vs QLFTest
edgeR
updated 8 weeks ago by 50k • written 9 weeks ago by • 0
2
votes
5
replies
1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
1
vote
6
replies
484
views
Library size normalization in methylation count analysis
edgeR MethylationArray
9 weeks ago mico • 0
5
votes
4
replies
389
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
11 weeks ago • updated 10 weeks ago pl23 • 0
0
votes
8
replies
630
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
11 weeks ago • updated 10 weeks ago Marianna ▴ 20
2
votes
6
replies
408
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
11 weeks ago • updated 10 weeks ago tsl0026 • 0
3
votes
2
replies
423
views
How does one test for interactions in EdgeR?
edgeR
12 weeks ago • updated 11 weeks ago pl23 • 0
1
vote
2
replies
324
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
12 weeks ago mico • 0
0
votes
4
replies
346
views
Nested paired design
edgeR
12 weeks ago manduchi ▴ 10
2
votes
3
replies
365
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
3
votes
4
replies
8.6k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 3 months ago by • 0 • written 10.8 years ago by ▴ 30
1
vote
8
replies
543
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 3 months ago by 50k • written 3 months ago by • 0
4
votes
4
replies
431
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by 65k • written 3 months ago by • 0
0
votes
5
replies
612
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
6
votes
7
replies
565
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
0
votes
0
replies
244
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
583
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
340
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
670
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
5
votes
7
replies
10.0k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 3 months ago by • 0 • written 7.1 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
You seem to have the misunderstanding that you can change the design matrix but keep all the other code unchanged. The contrasts are comput…
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
Awards • All
Popular Question to Gordon Smyth 50k
Popular Question to Zainab • 0
Popular Question to Theo ▴ 10
Popular Question to gene_bioconductor ▴ 10
Popular Question to rohitsatyam102 ▴ 20
Locations • All
United States, 1 minute ago
France, 2 minutes ago
United States, 3 minutes ago
WEHI, Melbourne, Australia, 3 minutes ago
San Diego, 9 minutes ago
Traffic: 550 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