Showing : edgeR • reset
4
votes
3
replies
1.2k
views
bias correction (an example from ChIP-seq)
normalization limma edgeR DEseq2
8.7 years ago Bogdan ▴ 670
1
vote
2
replies
2.0k
views
Trying to design a model(s) for a two factor RNA-seq experimental analysis in EdgeR with interaction
EdgeR RNAseq experimental design glm
updated 8.7 years ago by ★ 29k • written 8.7 years ago by • 0
4
votes
1
reply
1.5k
views
Should I adjust my q-values in edgeR/DESeq2 in my example?
edger deseq2
updated 8.7 years ago by 53k • written 8.7 years ago by ▴ 10
2
votes
1
reply
1.4k
views
Differences among phenotypes with different subgroups
design and contrast matrix statistical modeling edger DiffBind
updated 8.7 years ago by ★ 5.2k • written 8.7 years ago by ▴ 10
0
votes
2
replies
1.6k
views
Why all of the logFC are NA in my edgeDF2
R edger systemPipeR
8.7 years ago xuertowong • 0
1
vote
15
replies
3.0k
views
Edge R Issue from a basic differential expression analysis
edger
updated 8.7 years ago by 53k • written 8.7 years ago by • 0
0
votes
2
replies
1.9k
views
Using edgeR for small shRNA-seq screen analysis
edger shrna
8.7 years ago sirintra ▴ 10
3
votes
3
replies
1.4k
views
limma decideTests: only p-value less than (but not equal to) alpha are flagged as significant
limma edger significance rnaseq
updated 8.7 years ago by 53k • written 8.7 years ago by ▴ 20
3
votes
2
replies
4.0k
views
Using the ERCC spike as a normalization factor for a custom algorithm
ERCC rna-seq edgeR tmm normalised values
updated 8.7 years ago by ★ 29k • written 8.7 years ago by • 0
3
votes
6
replies
3.1k
views
Strange output from goana()
edger goana
updated 8.7 years ago by 53k • written 8.7 years ago by • 0
1
vote
4
replies
2.3k
views
Can edgeR be used on GO terms?
edger go rnaseq
8.7 years ago y.zhang36 • 0
6
votes
4
replies
2.9k
views
RNA-seq Normalisation - normalise all samples in experiment or only the ones used in the comparison?
rna-seq normalization edgeR limma
updated 8.8 years ago by 53k • written 8.8 years ago by • 0
2
votes
1
reply
2.4k
views
edgeR: time series analysis
edger time course
updated 8.8 years ago by 53k • written 8.8 years ago by ▴ 80
0
votes
1
reply
833
views
edgeR bcvvalue related significant number of genes
edger
updated 8.8 years ago by 53k • written 8.8 years ago by • 0
6
votes
4
replies
2.4k
views
apply edgeR TMM normalization without converting data format into 'DGEList'
edgeR tmm normalised values
updated 8.8 years ago by 53k • written 8.8 years ago by • 0
6
votes
6
replies
2.8k
views
correction for batch effects and paired-design of RNA-seq samples
limma edgeR
updated 8.8 years ago by 53k • written 8.8 years ago by ▴ 670
1
vote
3
replies
5.7k
views
edgeR::estimateDisp gives Error in qr.default(x) : NA/NaN/Inf in foreign function call (arg 1) (minimal working example included)
edgeR estimatedisp
8.8 years ago endrebak85 ▴ 40
4
votes
13
replies
2.7k
views
limma and edgeR QL strange results
limma limma voom edger
updated 8.8 years ago by ★ 7.9k • written 8.8 years ago by ▴ 10
3
votes
11
replies
12k
views
How to interpret plotBCV plots in edgeR
rnaseq edger
8.8 years ago davide.bau • 0
3
votes
2
replies
1.6k
views
edgeR QL with voom weights
edger limma-voom voom
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 10
0
votes
1
reply
990
views
Contrast Specific Dispersion Estimate
edgeR design and contrast matrix
8.8 years ago tk • 0
0
votes
5
replies
1.3k
views
selecting the right package for complex designs
limma edger lme4
updated 8.8 years ago by ★ 29k • written 8.8 years ago by • 0
0
votes
2
replies
981
views
classic vs GLM EDGER
edger
updated 8.8 years ago by ★ 29k • written 8.8 years ago by • 0
1
vote
4
replies
2.6k
views
EdgeR differentially expressed genes vs normal boxplot visualization
edgeR boxplot
8.8 years ago snowru • 0
0
votes
2
replies
2.7k
views
Unable to install DeSeq2 and EdgeR in ubuntu 16.04 , this is what happens when I install DeSeq2
deseq2 ubuntu edger dependencies
8.8 years ago aditya531996 • 0
4
votes
6
replies
3.8k
views
edgeR on DEG analysis: Size cannot be NA nor exceed 65536
edger differential gene expression
updated 8.8 years ago by 68k • written 8.8 years ago by • 0
3
votes
5
replies
5.9k
views
How to deal with low-depth RNA-Seq within DESeq2 or edgeR
rnaseq normalization differential gene expression edger deseq2
updated 8.8 years ago by ★ 7.9k • written 8.8 years ago by ▴ 90
4
votes
2
replies
1.2k
views
about model.matrix in limma or edgeR
limma edgeR
updated 8.8 years ago by 53k • written 8.8 years ago by ▴ 670
0
votes
2
replies
2.0k
views
Visualizing Normalization in DiffBind using MA: Differences between DESEQ2 / EdgeR & full v. effective library size
diffbind edger deseq2 chip-seq
updated 8.8 years ago by ★ 5.2k • written 8.8 years ago by • 0
1
vote
2
replies
1.2k
views
Removinf Batch effect in EDGE-R
R edger batch effect
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 40
0
votes
2
replies
1.1k
views
edgeR minor bug in normalizeChIPtoInput
edgeR
updated 8.8 years ago by 53k • written 8.8 years ago by • 0
3
votes
1
reply
2.0k
views
Hill in P-value distribution for heterogenous ChIP-seq samples
csaw limma sva qsmooth edger
updated 8.8 years ago by ★ 29k • written 8.8 years ago by ▴ 70
3
votes
6
replies
2.5k
views
Differential Pol2 pausing analysis
edger csaw chipseq differential binding analysis
updated 8.8 years ago by ★ 29k • written 8.8 years ago by • 0
3
votes
3
replies
2.1k
views
Use csaw to build matrix for heatmap?
csaw chipseq edger
updated 8.8 years ago by ★ 29k • written 8.8 years ago by • 0
2
votes
6
replies
4.6k
views
RNA-seq paired analysis design
paired samples design matrix limma deseq2 edger
updated 8.8 years ago by 53k • written 8.8 years ago by • 0
1
vote
2
replies
2.5k
views
How to use 'IHW' package to filter genes?
ihw deseq2 edger limma voom
updated 8.8 years ago by ▴ 610 • written 8.8 years ago by • 0
0
votes
1
reply
771
views
Bug Report: I think there is a typo in topTags() that interferes with the p.value argument functionality.
software error edgeR
updated 8.8 years ago by 53k • written 8.8 years ago by • 0
1
vote
1
reply
941
views
How to save output after normalizion using TMM
edger
updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 10
3
votes
7
replies
1.7k
views
searching for edgeR version 2.2.6
edgeR
updated 8.8 years ago by 25k • written 8.8 years ago by ▴ 10
2
votes
5
replies
1.6k
views
Including novel transcripts and antisense into differential gene expression analysis
edger rnaseq
updated 8.9 years ago by ★ 29k • written 8.9 years ago by • 0
4
votes
5
replies
2.9k
views
edgeR quasi-likelihood dispersion estimates
edger
updated 8.9 years ago by ★ 29k • written 8.9 years ago by • 0
25
votes
37
replies
16k
views
Possible ways of performing differential gene expression and analysis of RNA-Seq data from normalized counts of RSEM software
rnaseq RSEM TCGA edgeR normalization
updated 8.9 years ago by 53k • written 8.9 years ago by ▴ 840
1
vote
17
replies
2.7k
views
design for edgeR
edger design matrix glmlrt
updated 8.9 years ago by ★ 29k • written 8.9 years ago by • 0
1
vote
6
replies
1.6k
views
design of edgeR GLM test
edger differential gene expression glmlrt()
8.9 years ago simarsidhu25 • 0
1
vote
1
reply
1.4k
views
RNA-seq: EdgeR's togtags table not correlating to htseq-count's CPM values
edger htseqcounts rnaseq
updated 8.9 years ago by ★ 29k • written 8.9 years ago by • 0
4
votes
7
replies
3.5k
views
Can we use glmQLFit instead of glmFit and then glmLRT in edgeR
edger differential gene expression glmlrt()
8.9 years ago simarsidhu25 • 0
2
votes
7
replies
1.8k
views
diffHic: minimum counts per bin
diffhic edger
8.9 years ago andreucat91 • 0
4
votes
4
replies
3.0k
views
edgeR: Unusual BCV plot
edger
updated 8.9 years ago by 53k • written 8.9 years ago by • 0
3
votes
6
replies
1.8k
views
edgeR and variance
edger
updated 8.9 years ago by 53k • written 10.1 years ago by • 0
2
votes
1
reply
1.2k
views
cpm filtering edgeR
edger
updated 8.9 years ago by ★ 29k • written 8.9 years ago by ▴ 20
2,031 results • Page 21 of 41
Recent ...
Replies
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much, @ATpoint and @kevin , for your valuable insights. I have carefully checked all your suggestions. First, I examined th…
Answer: Finding duplicated entries in GRangesList by Kevin Blighe ★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: DESeq2 on non-RNASeq counts data by Kevin Blighe ★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
Votes
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
Awards • All
Scholar to Gordon Smyth 53k
Popular Question to shepherl 4.2k
Supporter to fabio.marroni • 0
Popular Question to Guido Hooiveld ★ 4.1k
Popular Question to James W. MacDonald 68k
Locations • All
Germany, just now
WEHI, Melbourne, Australia, 4 minutes ago
Pittsburgh, United States, 1 hour ago
United States, 3 hours ago
United States, 4 hours ago
Traffic: 626 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