Showing : edgeR • reset
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6
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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
3.0k
views
EdgeR glmLRT vs glmQLFTest
edgeR DifferentialExpression
updated 8 months ago by • 0 • written 3.1 years ago by ▴ 20
2
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3
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838
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Import Salmon data with tximport and pool technical replicates
tximport edgeR
written 9 months ago by • 0
0
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9
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872
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estimateDisp() error
edgeR
updated 9 months ago by 50k • written 9 months ago by • 0
1
vote
5
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696
views
edgeR design/contrast matrix troubles
edgeR
updated 8 months ago by 65k • written 8 months ago by • 0
2
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5
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1.4k
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Question about RNAseq analysis in EdgeR to identify common and donor specific differentially expressed genes
R edgeR RNASeq
10 months ago • updated 9 months ago mohammedtoufiq91 ▴ 10
3
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4
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8.7k
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Gene-gene correlation analysis with RNA-seq
edgeR
updated 3 months ago by • 0 • written 10.9 years ago by ▴ 30
0
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4
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919
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Handle zero effective gene length when tximport RSEM results
tximport edgeR
updated 8 months ago by 42k • written 9 months ago by • 0
1
vote
3
replies
368
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
1
vote
2
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458
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EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
4
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4
replies
457
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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
6
replies
370
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
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
6
votes
7
replies
970
views
[Bug] Segfault in edgeR::cpm
edgeR segfault
updated 6 months ago by ★ 4.1k • written 7 months 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
0
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3
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480
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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
368
views
permutation test in edgeR
rna-seq edgeR
updated 27 days ago by 50k • written 5 weeks ago by • 0
1
vote
4
replies
761
views
MDS plot edgeR
edgeR
updated 8 months ago by 50k • written 8 months ago by ▴ 10
5
votes
9
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2.5k
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
0
votes
2
replies
305
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RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
9
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12
replies
7.9k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 29 days ago by • 0 • written 8.9 years ago by ▴ 30
4
votes
9
replies
1.4k
views
RNA seq differential expression analysis for large sample size
edgeR DESeq2
9 months ago Luca • 0
1
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5
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882
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
9 months ago duez.tolga • 0
2
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8
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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
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3
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439
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Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
0
votes
2
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501
views
EdgeR FTest
edgeR
updated 9 months ago by 50k • written 9 months ago by • 0
5
votes
2
replies
600
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
3
replies
305
views
Log-cpm values from limma
limma edgeR RNASeq
updated 8 days ago by 50k • written 4 weeks ago by • 0
3
votes
3
replies
570
views
EdgeR and DESeq2, variance estimation and parametric test
parametrictest edgeR DESeq2
8 months ago Nisha • 0
1
vote
1
reply
409
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
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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
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
6
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469
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FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 25 days ago Jonathan ▴ 10
1
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5
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757
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
0
votes
1
reply
250
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
2
votes
4
replies
648
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
438
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
3 months ago • updated 12 weeks ago tsl0026 • 0
0
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2
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1.1k
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library size and fold changes
edgeR edgeR
updated 7 weeks ago by 50k • written 12.5 years ago by ▴ 670
1
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2
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493
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
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
2
votes
3
replies
386
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 months ago by • 0
5
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4
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429
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
3 months ago • updated 12 weeks ago pl23 • 0
2
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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
0
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2
replies
147
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
29 days ago prity6459 • 0
0
votes
1
reply
511
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
votes
1
reply
613
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
7
votes
2
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862
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
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11
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2.9k
views
edgeR contrasts
edgeR
updated 9 months ago by 65k • written 20 months ago by • 0
2
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5
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1.4k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
4
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2
replies
620
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
15 days ago • updated 11 days ago gene_bioconductor ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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