Showing : EdgeR • reset
1
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6
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2.7k
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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
2
votes
7
replies
2.9k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.0 years ago by ▴ 20
2
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3
replies
811
views
Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 8 months ago by • 0
0
votes
9
replies
846
views
estimateDisp() error
edgeR
updated 9 months ago by 50k • written 9 months ago by • 0
4
votes
4
replies
431
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edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by 65k • written 3 months ago by • 0
9
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5
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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
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
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
1
vote
3
replies
347
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 20 days ago by 50k • written 25 days ago by • 0
1
vote
2
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418
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
1
vote
4
replies
735
views
MDS plot edgeR
edgeR
updated 7 months ago by 50k • written 7 months ago by ▴ 10
0
votes
6
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355
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 5 weeks ago by 50k • written 5 weeks 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
6
votes
7
replies
949
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 6 months ago by ★ 4.1k • written 6 months ago by ▴ 20
4
votes
7
replies
13k
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
0
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3
replies
458
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'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
5 months ago Karthik • 0
3
votes
3
replies
333
views
permutation test in edgeR
rna-seq edgeR
updated 14 days ago by 50k • written 27 days ago by • 0
0
votes
4
replies
883
views
Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 8 months ago by 41k • written 8 months ago by • 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
2
replies
281
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
4
votes
9
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1.3k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
9
votes
12
replies
7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 16 days ago by • 0 • written 8.8 years ago by ▴ 30
1
vote
5
replies
676
views
edgeR design/contrast matrix troubles
edgeR
updated 7 months ago by 65k • written 8 months ago by • 0
1
vote
5
replies
855
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
9 months ago • updated 8 months ago duez.tolga • 0
1
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3
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405
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
0
votes
2
replies
478
views
EdgeR FTest
edgeR
updated 8 months ago by 50k • written 8 months ago by • 0
5
votes
2
replies
558
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 4 months ago by 50k • written 5 months ago by • 0
3
votes
1
reply
173
views
Log-cpm values from limma
limma edgeR RNASeq
updated 16 days ago by 50k • written 17 days ago by • 0
3
votes
3
replies
547
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
7 months ago Nisha • 0
1
vote
1
reply
403
views
A query about selecting the coefficient in glmLRT to test for by index
edgeR
updated 9 months ago by 50k • written 9 months ago by • 0
4
votes
12
replies
3.7k
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
3
replies
1.8k
views
catchSalmon for tx-level DE
catchSalmon edgeR
updated 5 months ago by 50k • written 3.5 years ago by ★ 4.1k
4
votes
6
replies
426
views
FilterByExpr low counts with small sample size
edgeR
17 days ago • updated 12 days ago Jonathan ▴ 10
1
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5
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737
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
0
votes
11
replies
2.8k
views
edgeR contrasts
edgeR
updated 8 months ago by 65k • written 20 months ago by • 0
2
votes
1
reply
602
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
0
votes
1
reply
233
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
2
votes
6
replies
411
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
11 weeks ago • updated 10 weeks ago tsl0026 • 0
0
votes
2
replies
1.1k
views
library size and fold changes
edgeR edgeR
updated 5 weeks ago by 50k • written 12.4 years ago by ▴ 670
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
0
votes
2
replies
132
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
16 days ago prity6459 • 0
5
votes
4
replies
394
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
11 weeks ago • updated 10 weeks ago pl23 • 0
2
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2
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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
7
votes
2
replies
805
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
2
votes
3
replies
367
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 12 weeks ago by 65k • written 12 weeks ago by • 0
0
votes
1
reply
499
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
2
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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
4
replies
587
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
1
vote
1
reply
274
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
updated 2 days ago by 50k • written 2 days ago by ▴ 10
0
votes
1
reply
1.5k
views
EdgeR norm.factor input
Normalization edgeR Normalization edgeR
updated 4 months ago by 50k • written 10.2 years ago by ★ 13k
50 results • Page 1 of 1
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Comment: Too many significant genes when integrating gtex and tcga by ATpoint ★ 4.1k
These two datasets are from completely different experiments / batches. It is utterly meaningless to compare them. I would suggest comparat…
Answer: fgsea significant result by ATpoint ★ 4.1k
Set a fixed seed before running this. Note that a FDR of 0.25 in fgsea is wildly and overly lenient. See https://support.bioconductor.o…
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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