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
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 20 days ago by • 0 • written 8.8 years ago by ▴ 30
5
votes
11
replies
3.1k
views
Visualization of negative log CPM values
Visualization Normalization ggplot2 edgeR
written 11 months ago by ▴ 20
0
votes
11
replies
2.8k
views
edgeR contrasts
edgeR
updated 9 months ago by 65k • written 20 months ago by • 0
0
votes
11
replies
744
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 9 weeks ago by 50k • written 10 weeks ago by • 0
6
votes
10
replies
1.7k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 19 days ago by • 0 • written 15 months ago by ▴ 10
4
votes
9
replies
1.3k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
0
votes
9
replies
852
views
estimateDisp() error
edgeR
updated 9 months ago by 50k • written 9 months ago by • 0
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
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
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
1.4k
views
Question about filterByExpr function edgeR
edgeR
8 months ago lucap • 0
1
vote
8
replies
551
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
650
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
12 weeks ago • updated 11 weeks ago Marianna ▴ 20
6
votes
7
replies
955
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 6 months ago by ★ 4.1k • written 6 months ago by ▴ 20
2
votes
7
replies
3.0k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.0 years ago by ▴ 20
6
votes
7
replies
578
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
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
4
votes
7
replies
14k
views
Confused about the CPM and TMM normalization in edgeR
RNASeq R edgeR
updated 7 months ago by 50k • written 22 months ago by ▴ 30
5
votes
6
replies
434
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 25 days ago by ★ 4.1k • written 29 days ago by ▴ 30
4
votes
6
replies
441
views
FilterByExpr low counts with small sample size
edgeR
21 days ago • updated 16 days ago Jonathan ▴ 10
2
votes
6
replies
419
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
11 weeks ago tsl0026 • 0
0
votes
6
replies
362
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
3
votes
6
replies
844
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
1
vote
6
replies
497
views
Library size normalization in methylation count analysis
edgeR MethylationArray
10 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
740
views
Why do I obtain Identical Adj.P value when running edgeR ?
edgeR
updated 7 months ago by 50k • written 7 months ago by ▴ 30
3
votes
5
replies
390
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
1
vote
5
replies
861
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
9 months ago • updated 8 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
800
views
Model and Contrasts with 4 variables
contrast edgeR DESeq2
updated 11 months ago by 65k • written 11 months ago by • 0
0
votes
5
replies
626
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
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 5 weeks ago by 50k • written 11.5 years ago by ▴ 30
1
vote
5
replies
681
views
edgeR design/contrast matrix troubles
edgeR
updated 8 months ago by 65k • written 8 months 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
601
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
0
votes
4
replies
891
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
4
replies
404
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
11 weeks ago • updated 10 weeks ago pl23 • 0
1
vote
4
replies
746
views
MDS plot edgeR
edgeR
updated 7 months ago by 50k • written 7 months ago by ▴ 10
3
votes
4
replies
711
views
Anova table edgeR limma
limma RNASeq edgeR
12 months ago KATHERINE CHUERE NUNES • 0
4
votes
4
replies
437
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
4
replies
355
views
Nested paired design
edgeR
3 months ago manduchi ▴ 10
3
votes
4
replies
439
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
0
votes
4
replies
436
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
5 weeks ago Lucy ▴ 60
3
votes
3
replies
551
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
7 months ago Nisha • 0
0
votes
3
replies
460
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
3
votes
3
replies
576
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 7 months ago by 65k • written 7 months ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: EGSEA usage with microarray data (with vooma)? by Chris • 0
Hi Pekka, I also try EGSEA with microarray data. However, I got this error. Would you please have a suggestion? gsa = egsea.ma(numeric…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
> Any suggestions for methylation data segmentation? I think the same segmentation can be used.
Comment: deseq2 results by swbarnes2 ★ 1.3k
Cross-posted https://www.biostars.org/p/9594331/#9594458
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Mike Smith ★ 6.5k
The other answers here are all good and demonstrate the issue with floating point comparisons nicely. I'd like to add that your particular…
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70
Nudging my question. I could do with confirmation before proceeding with my current projects. Thank you.
Votes
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: minfi latest update for EPIC V2 chip
A: Error in DESeqDataSet : some values in assay are not integers
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