Showing : EdgeR • reset
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
9
votes
12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 27 days ago by • 0 • written 8.9 years ago by ▴ 30
0
votes
11
replies
2.9k
views
edgeR contrasts
edgeR
updated 9 months ago by 65k • written 20 months ago by • 0
0
votes
11
replies
769
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 10 weeks ago by 50k • written 11 weeks ago by • 0
5
votes
11
replies
3.2k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 11 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 26 days ago by • 0 • written 15 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 Luca • 0
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
0
votes
9
replies
864
views
estimateDisp() error
edgeR
updated 9 months ago by 50k • written 9 months ago by • 0
4
votes
9
replies
1.4k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
1
vote
8
replies
568
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 3 months ago by 50k • written 3 months ago by • 0
0
votes
8
replies
1.4k
views
Question about filterByExpr function edgeR
edgeR
9 months ago • updated 8 months ago lucap • 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
0
votes
8
replies
673
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
3 months ago • updated 12 weeks ago Marianna ▴ 20
6
votes
7
replies
963
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 6 months ago by ★ 4.1k • written 7 months ago by ▴ 20
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
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
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
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
6
votes
7
replies
593
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
6
replies
453
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 4 weeks ago by ★ 4.1k • written 5 weeks ago by ▴ 30
4
votes
6
replies
460
views
FilterByExpr low counts with small sample size
edgeR
28 days ago • updated 23 days ago Jonathan ▴ 10
2
votes
6
replies
434
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
12 weeks ago tsl0026 • 0
3
votes
6
replies
854
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
0
votes
6
replies
369
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
1
vote
6
replies
519
views
Library size normalization in methylation count analysis
edgeR MethylationArray
11 weeks ago mico • 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
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
1
vote
5
replies
753
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
1
vote
5
replies
874
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
9 months ago duez.tolga • 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
0
votes
5
replies
639
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
0
votes
5
replies
814
views
Model and Contrasts with 4 variables
contrast edgeR DESeq2
updated 11 months ago by 65k • written 11 months ago by • 0
1
vote
5
replies
694
views
edgeR design/contrast matrix troubles
edgeR
updated 8 months ago by 65k • written 8 months ago by • 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
9 months ago mohammedtoufiq91 ▴ 10
0
votes
5
replies
1.8k
views
EdgeR: paired samples together with independant samples
RNASeq edgeR RNASeq edgeR
updated 6 weeks ago by 50k • written 11.5 years ago by ▴ 30
3
votes
5
replies
408
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
2
votes
4
replies
633
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
1
vote
4
replies
760
views
MDS plot edgeR
edgeR
updated 7 months ago by 50k • written 7 months ago by ▴ 10
5
votes
4
replies
420
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
12 weeks ago • updated 11 weeks ago pl23 • 0
0
votes
4
replies
362
views
Nested paired design
edgeR
3 months ago manduchi ▴ 10
4
votes
4
replies
450
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
0
votes
4
replies
446
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
6 weeks ago Lucy ▴ 60
3
votes
4
replies
486
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 10 weeks ago by 50k • written 10 weeks ago by ▴ 50
0
votes
4
replies
914
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 8 months ago by 42k • written 8 months ago by • 0
5
votes
3
replies
302
views
Log-cpm values from limma
limma edgeR RNASeq
updated 5 days ago by 50k • written 27 days ago by • 0
3
votes
3
replies
564
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
8 months ago Nisha • 0
0
votes
3
replies
477
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
1
vote
3
replies
436
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly? by pangtaihin • 0
Thank you:)
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly? by pangtaihin • 0
Thank you! But I apologize for cannot fully grasp your point. Do you mean that when the counts are high, rlogged matrix can represent the t…
Comment: Query regarding phyloseq object construct with QIIME output by Rosso • 0
Constructing a phyloseq object from QIIME output involves several steps to integrate taxonomic abundance data, sample metadata, and phyloge…
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Marcel Ramos 690
`BiocManager` does not install local packages. It only installs Bioconductor, CRAN, and GitHub ones. You should install local packages w…
Comment: error running enricher from clusterprofiler by Yael • 0
It worked!!! Thanks alot, i think something in the gene_list wasnt right... Thanks agian
Votes
Answer: Can DESeq2 rlog normalized matrix reflects time course result directly?
Comment: Can DESeq2 rlog normalized matrix reflects time course result directly?
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Answer: Trim/Filter out-of-bounds GRanges
Comment: How to correctly adjust for gender in edgeR
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