Showing : edgeR • reset
9
votes
5
replies
5.1k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 5 months ago by 50k • written 8.2 years ago by ▴ 90
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 23 days ago by • 0 • written 8.8 years ago by ▴ 30
7
votes
2
replies
829
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 5 months ago by 50k • written 5 months ago by • 0
6
votes
2
replies
728
views
How to access the C++ code of the function .cxx_ave_log_cpm in the aveLogCPM.default function of EdgeR package?
edgeR
10 months ago Josué ▴ 20
6
votes
7
replies
957
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 6 months ago by ★ 4.1k • written 6 months ago by ▴ 20
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 22 days ago by • 0 • written 15 months ago by ▴ 10
6
votes
7
replies
585
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
5
votes
11
replies
3.1k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 11 months ago by ▴ 20
5
votes
6
replies
445
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 29 days ago by ★ 4.1k • written 4 weeks ago by ▴ 30
5
votes
2
replies
586
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 5 months ago by 50k • written 5 months ago by • 0
5
votes
4
replies
410
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
12 weeks ago • updated 11 weeks ago pl23 • 0
5
votes
3
replies
727
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 6 weeks ago by 50k • written 7 weeks ago by ▴ 50
5
votes
9
replies
2.5k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger calcnormfactors
updated 8 months ago by • 0 • written 6.5 years ago by ▴ 10
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 11 months ago by 50k • written 11 months ago by ▴ 10
5
votes
7
replies
10k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 3 months ago by • 0 • written 7.1 years ago by • 0
5
votes
3
replies
275
views
Log-cpm values from limma
limma edgeR RNASeq
updated 2 days ago by 50k • written 24 days ago by • 0
4
votes
12
replies
3.8k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
updated 7 months ago by • 0 • written 3.2 years ago by • 0
4
votes
6
replies
449
views
FilterByExpr low counts with small sample size
edgeR
24 days ago • updated 19 days ago Jonathan ▴ 10
4
votes
3
replies
1.8k
views
catchSalmon for tx-level DE
catchSalmon edgeR
updated 6 months ago by 50k • written 3.6 years ago by ★ 4.1k
4
votes
9
replies
1.3k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
4
votes
2
replies
587
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
9 days ago • updated 5 days ago gene_bioconductor ▴ 10
4
votes
4
replies
443
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by 65k • written 4 months ago by • 0
4
votes
7
replies
14k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 8 months ago by 50k • written 22 months ago by ▴ 30
4
votes
2
replies
652
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 6 months ago by 50k • written 6 months ago by ▴ 10
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
4 months ago • updated 3 months ago Luca • 0
4
votes
3
replies
1.0k
views
Custom design for scRNA DGE with pseudobulking
scRNAseq scrna paireddesign edgeR pseudobulking
updated 9 months ago by 50k • written 9 months ago by • 0
3
votes
3
replies
556
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
8 months ago Nisha • 0
3
votes
2
replies
469
views
How does one test for interactions in EdgeR?
edgeR
3 months ago • updated 12 weeks ago pl23 • 0
3
votes
5
replies
398
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 6 weeks ago by 50k • written 6 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 10.9 years ago by ▴ 30
3
votes
2
replies
681
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 10 months ago by 50k • written 10 months ago by ▴ 10
3
votes
1
reply
1.7k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 4 months ago by 50k • written 3.0 years ago by ▴ 60
3
votes
6
replies
850
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 11 months ago by 50k • written 11 months ago by ▴ 10
3
votes
3
replies
692
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
3
votes
3
replies
583
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 7 months ago by 65k • written 7 months ago by • 0
3
votes
4
replies
459
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 9 weeks ago by 50k • written 9 weeks ago by ▴ 50
3
votes
3
replies
356
views
permutation test in edgeR
rna-seq edgeR
updated 21 days ago by 50k • written 4 weeks ago by • 0
2
votes
2
replies
273
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
8 weeks ago Sabiha ▴ 20
2
votes
3
replies
301
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
2
votes
4
replies
613
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
2
votes
6
replies
424
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
12 weeks ago • updated 11 weeks ago tsl0026 • 0
2
votes
2
replies
2.0k
views
humann2 output appropriate for EdgeR or DESeq2 analysis
edger deseq2
updated 8 months ago by • 0 • written 6.4 years ago by • 0
2
votes
3
replies
379
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
2
votes
3
replies
830
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 8 months 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
2
votes
1
reply
606
views
DESeq2 or edgeR for Presence and Absence of Proteins
edgeR DESeq2
updated 11 months ago by ★ 4.1k • written 11 months ago by • 0
2
votes
8
replies
2.3k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
13 months ago • updated 11 months ago Luis • 0
2
votes
7
replies
3.0k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.1 years ago by ▴ 20
2
votes
5
replies
1.4k
views
Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
9 months ago mohammedtoufiq91 ▴ 10
2
votes
2
replies
264
views
between lane normalization upper quantile
EDASeq edgeR
8 weeks ago • updated 7 weeks ago elesofi • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ziliang • 0
I am so confused and frustrated learning to use this software. Isn't how you merge the peaksets one of the most important steps for the com…
Answer: SingleR Label.Ont by Denis • 0
[Jackpot City Casino][1] is the perfect option when looking for an online casino in Canada for an exciting vacation and huge winnings that …
Comment: deseq2 results by sajadahmad41454 • 0
thank you so much and sorry for bothering you again and again, it is urgent because it is my project deadline. i have removed that sample a…
Comment: deseq2 results by swbarnes2 ★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code? by NATASHA • 0
did you find a solution? I´m having the same problem
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
Awards • All
Popular Question to maria.soler • 0
Popular Question to Pietro ▴ 40
Popular Question to neilzhao ▴ 30
Popular Question to ATpoint ★ 4.1k
Teacher to Michael Love 42k
Locations • All
France, 18 minutes ago
United Kingdom, 39 minutes ago
Poland, 1 hour ago
the United States, 1 hour ago
WEHI, Melbourne, Australia, 1 hour ago
Traffic: 399 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