Showing : edgeR • reset
1
vote
1
reply
244
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 2 days ago by 50k • written 2 days ago by ▴ 10
0
votes
1
reply
89
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 2 days ago by 50k • written 2 days ago by • 0
1
vote
1
reply
176
views
Citation for edgeR user guide
edgeR
updated 11 days ago by 50k • written 11 days ago by ▴ 30
4
votes
6
replies
426
views
FilterByExpr low counts with small sample size
edgeR
17 days ago • updated 12 days ago Jonathan ▴ 10
3
votes
3
replies
332
views
permutation test in edgeR
rna-seq edgeR
updated 14 days ago by 50k • written 26 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 15 days ago by • 0 • written 15 months ago by ▴ 10
0
votes
3
replies
188
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 15 days ago by 50k • written 16 days ago by • 0
0
votes
2
replies
132
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
15 days ago prity6459 • 0
3
votes
1
reply
173
views
Log-cpm values from limma
limma edgeR RNASeq
updated 15 days ago by 50k • written 16 days ago by • 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 16 days ago by • 0 • written 8.8 years ago by ▴ 30
1
vote
3
replies
347
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 19 days ago by 50k • written 24 days ago by • 0
5
votes
6
replies
425
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 21 days ago by ★ 4.1k • written 25 days ago by ▴ 30
1
vote
3
replies
248
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 29 days ago by 65k • written 29 days ago by • 0
0
votes
2
replies
167
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
4 weeks ago Marianna ▴ 20
0
votes
4
replies
420
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
383
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 5 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 5 weeks ago by 50k • written 12.4 years ago by ▴ 670
0
votes
6
replies
355
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
712
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
293
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 7 weeks ago by 50k • written 7 weeks ago by • 0
2
votes
2
replies
262
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
404
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
428
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
738
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
220
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
254
views
ExactTest vs QLFTest
edgeR
updated 9 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
492
views
Library size normalization in methylation count analysis
edgeR MethylationArray
9 weeks ago mico • 0
5
votes
4
replies
394
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
11 weeks ago • updated 10 weeks ago pl23 • 0
0
votes
8
replies
636
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
411
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
11 weeks ago • updated 10 weeks ago tsl0026 • 0
3
votes
2
replies
428
views
How does one test for interactions in EdgeR?
edgeR
12 weeks ago • updated 11 weeks ago pl23 • 0
1
vote
2
replies
326
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
12 weeks ago mico • 0
0
votes
4
replies
350
views
Nested paired design
edgeR
12 weeks ago manduchi ▴ 10
2
votes
3
replies
367
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
548
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
614
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
6
votes
7
replies
566
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
245
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
585
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
341
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
673
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: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
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 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
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…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
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
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
France, 20 minutes ago
India, 1 hour ago
The city by the bay, 2 hours ago
WEHI, Melbourne, Australia, 4 hours ago
United States, 4 hours ago
Traffic: 508 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