Showing : EdgeR • reset
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 23 months ago by ▴ 30
5
votes
7
replies
10k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 4 months ago by • 0 • written 7.2 years ago by • 0
3
votes
4
replies
8.7k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 3 months ago by • 0 • written 10.9 years ago by ▴ 30
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 5 weeks ago by • 0 • written 8.9 years ago by ▴ 30
9
votes
5
replies
5.1k
views
Differential expression analysis: Permutation Test
deseq2 limma edger permutation
updated 6 months ago by 50k • written 8.3 years ago by ▴ 90
4
votes
12
replies
3.8k
views
Using edgeR and a spike-in to calculate absolute abundance
edgeR SpikeIn RNASeq
updated 8 months ago by • 0 • written 3.2 years ago by • 0
5
votes
11
replies
3.3k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 12 months ago by ▴ 20
2
votes
7
replies
3.0k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 9 months ago by • 0 • written 3.1 years ago by ▴ 20
0
votes
11
replies
3.0k
views
edgeR contrasts
edgeR
updated 9 months ago by 66k • written 20 months ago by • 0
1
vote
6
replies
2.7k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 7.5 years ago by ▴ 10
5
votes
9
replies
2.6k
views
edgeR: Should there be a normalization step for CRISPR screens? How to deal with bottlenecked screens?
edger calcnormfactors
updated 9 months ago by • 0 • written 6.5 years ago by ▴ 10
2
votes
8
replies
2.4k
views
Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
13 months ago • updated 12 months ago Luis • 0
2
votes
2
replies
2.0k
views
humann2 output appropriate for EdgeR or DESeq2 analysis
edger deseq2
updated 9 months ago by • 0 • written 6.4 years ago by • 0
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 ★ 4.2k
0
votes
5
replies
1.8k
views
EdgeR: paired samples together with independant samples
RNASeq edgeR RNASeq edgeR
updated 7 weeks ago by 50k • written 11.6 years ago by ▴ 30
6
votes
10
replies
1.8k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 5 weeks ago by • 0 • written 15 months ago by ▴ 10
3
votes
1
reply
1.8k
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 3.1 years ago by ▴ 60
0
votes
1
reply
1.5k
views
EdgeR norm.factor input
Normalization edgeR Normalization edgeR
updated 5 months ago by 50k • written 10.3 years ago by ★ 13k
2
votes
5
replies
1.5k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 15 months ago by • 0
0
votes
8
replies
1.5k
views
Question about filterByExpr function edgeR
edgeR
9 months ago lucap • 0
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
10 months ago mohammedtoufiq91 ▴ 10
4
votes
9
replies
1.4k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
10 months ago Luca • 0
0
votes
3
replies
1.3k
views
EdgeR glm based analysis
edgeR edgeR
10.4 years ago • updated 9 months ago Gordon Smyth 50k
4
votes
9
replies
1.2k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
4 months ago Luca • 0
0
votes
2
replies
1.1k
views
library size and fold changes
edgeR edgeR
updated 8 weeks ago by 50k • written 12.5 years ago by ▴ 670
4
votes
3
replies
1.1k
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
0
votes
0
replies
1.0k
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
9 months ago • updated 8 months ago Gordon Smyth 50k
6
votes
7
replies
989
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 7 months ago by ★ 4.2k • written 7 months ago by ▴ 20
0
votes
4
replies
946
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 9 months ago by 42k • written 9 months ago by • 0
1
vote
5
replies
900
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
9 months ago duez.tolga • 0
7
votes
2
replies
898
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
0
votes
9
replies
879
views
estimateDisp() error
edgeR
updated 9 months ago by 50k • written 9 months ago by • 0
3
votes
6
replies
868
views
Question on constructing design matrix and defining contrasts for analysis
wgcna DESeq2 edgeR limma design
updated 12 months ago by 50k • written 12 months ago by ▴ 10
1
vote
2
replies
861
views
Should I use CPM or Voom transformed values for downstream analysis?
edgeR limma
8 months ago petertam1343 • 0
2
votes
3
replies
852
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 9 months ago by • 0
0
votes
5
replies
833
views
Model and Contrasts with 4 variables
contrast edgeR DESeq2
updated 11 months ago by 66k • written 11 months ago by • 0
0
votes
11
replies
818
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 11 weeks ago by 50k • written 3 months ago by • 0
1
vote
4
replies
772
views
MDS plot edgeR
edgeR
updated 8 months ago by 50k • written 8 months ago by ▴ 10
1
vote
5
replies
769
views
Why do I obtain Identical Adj.P value when running edgeR ?
edgeR
updated 8 months ago by 50k • written 8 months ago by ▴ 30
5
votes
3
replies
767
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 8 weeks ago by 50k • written 9 weeks ago by ▴ 50
6
votes
2
replies
756
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
3
votes
3
replies
746
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
0
votes
2
replies
720
views
EdgeR and repeated measures: how to design a correct matrix having three time points
repeatedmeasure edgeR
9 months ago greta • 0
1
vote
5
replies
707
views
edgeR design/contrast matrix troubles
edgeR
updated 8 months ago by 66k • written 8 months ago by • 0
4
votes
2
replies
704
views
DecideTest vs topTAGs in edgeR
RNAseq StatisticalMethod edgeR
updated 7 months ago by 50k • written 7 months ago by ▴ 10
0
votes
8
replies
698
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
3 months ago Marianna ▴ 20
3
votes
2
replies
693
views
Does this RNAseq experiment require a repeated measures approach?
StatisticalMethod RNASeqData edgeR DESeq2
updated 11 months ago by 50k • written 11 months ago by ▴ 10
2
votes
4
replies
671
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago Sabiha ▴ 20
4
votes
2
replies
660
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
25 days ago • updated 21 days ago gene_bioconductor ▴ 10
0
votes
5
replies
656
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago Lucy ▴ 60
50 results • Page 1 of 1
Recent ...
Replies
Comment: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)? by ATpoint ★ 4.2k
I don't have an answer to the "why" but maybe a simple reimplemention will do: ```r seqs <- c("ATCATCGTATCAAAGTC", "AAAACGTATCAAAGTC", "TG…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by Guido Hooiveld ★ 4.0k
After checking `?DESeqDataSetFromMatrix` note this information: arguments provided to SummarizedExperiment including rowRanges and met…
Answer: Error in gseDO function by Guido Hooiveld ★ 4.0k
Yes, you are missing something. :-) For a GSEA you will need to use as input all genes that you are analyzing; these genes should be ran…
Comment: GSVA function by Robert Castelo ★ 3.3k
No, negative values may occur after log transformation when the `log(x)` is taken from a positive number `x with 0 < x < 1`, and therefore …
Comment: conumee with Infinium MethylationEPIC v2.0 by sgomez • 0
Hi Max, Could you try this? https://support.bioconductor.org/p/9136138/#9136840
Votes
A: Comparison between two different group's pathway analysis results
DiffBind Batch Effect
A: DiffBind Batch Effect
A: DiffBind Batch Effect
C: DiffBind Batch Effect
Awards • All
Popular Question to Robert Castelo ★ 3.3k
Popular Question to kevin.rue ▴ 350
Popular Question to Wei Shi ★ 3.6k
Popular Question to Gordon Smyth 50k
Popular Question to jovel_juan ▴ 30
Locations • All
The city by the bay, 19 minutes ago
United States, 25 minutes ago
United States, 49 minutes ago
Melbourne, Australia, 49 minutes ago
WEHI, Melbourne, Australia, 53 minutes ago
Traffic: 406 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