Showing : edger • reset
1
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1
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37
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Citation for edgeR user guide
edgeR
updated 6 hours ago by 50k • written 10 hours ago by ▴ 30
3
votes
6
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311
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FilterByExpr low counts with small sample size
edgeR
6 days ago • updated 1 day ago Jonathan ▴ 10
3
votes
3
replies
280
views
permutation test in edgeR
rna-seq edgeR
updated 3 days ago by 50k • written 15 days ago by • 0
6
votes
10
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1.5k
views
Which input file is used for DGEList in EgdeR?
salmon edgeR tximport nf-core gene_counts
updated 4 days ago by • 0 • written 14 months ago by ▴ 10
0
votes
3
replies
123
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 4 days ago by 50k • written 5 days ago by • 0
0
votes
2
replies
85
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
4 days ago prity6459 • 0
0
votes
1
reply
105
views
Log-cpm values from limma
limma edgeR RNASeq
updated 4 days ago by 50k • written 5 days ago by • 0
9
votes
12
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7.8k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 5 days ago by • 0 • written 8.8 years ago by ▴ 30
1
vote
3
replies
317
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 8 days ago by 50k • written 13 days ago by • 0
5
votes
6
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391
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 10 days ago by ★ 4.0k • written 14 days ago by ▴ 30
1
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3
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227
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 18 days ago by 65k • written 18 days ago by • 0
0
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2
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144
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edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
20 days ago Marianna ▴ 20
0
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4
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390
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
22 days ago • updated 21 days ago Lucy ▴ 60
0
votes
5
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1.8k
views
EdgeR: paired samples together with independant samples
RNASeq edgeR RNASeq edgeR
updated 22 days ago by 50k • written 11.5 years ago by ▴ 30
3
votes
5
replies
334
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 24 days ago by 50k • written 26 days ago by • 0
0
votes
2
replies
1.1k
views
library size and fold changes
edgeR edgeR
updated 24 days ago by 50k • written 12.4 years ago by ▴ 670
0
votes
6
replies
310
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 25 days ago by 50k • written 26 days ago by • 0
5
votes
3
replies
681
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 27 days ago by 50k • written 4 weeks ago by ▴ 50
0
votes
1
reply
214
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
2
votes
3
replies
276
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
2
votes
2
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241
views
between lane normalization upper quantile
EDASeq edgeR
5 weeks ago elesofi • 0
0
votes
2
replies
254
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 5 weeks ago by 50k • written 5 weeks ago by • 0
2
votes
2
replies
243
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
5 weeks ago Sabiha ▴ 20
0
votes
3
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358
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 11 weeks ago by • 0
3
votes
4
replies
393
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 6 weeks ago by 50k • written 7 weeks ago by ▴ 50
0
votes
11
replies
694
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 7 weeks ago by 50k • written 8 weeks ago by • 0
0
votes
1
reply
210
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
0
votes
1
reply
236
views
ExactTest vs QLFTest
edgeR
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
2
votes
5
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1.3k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 14 months ago by • 0
1
vote
6
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447
views
Library size normalization in methylation count analysis
edgeR MethylationArray
8 weeks ago mico • 0
5
votes
4
replies
373
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
9 weeks ago • updated 8 weeks ago pl23 • 0
0
votes
8
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601
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Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
10 weeks ago • updated 9 weeks ago Marianna ▴ 20
2
votes
6
replies
388
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
9 weeks ago tsl0026 • 0
3
votes
2
replies
380
views
How does one test for interactions in EdgeR?
edgeR
10 weeks ago pl23 • 0
1
vote
2
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303
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
10 weeks ago mico • 0
0
votes
4
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321
views
Nested paired design
edgeR
10 weeks ago manduchi ▴ 10
2
votes
3
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347
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 11 weeks ago by 65k • written 11 weeks ago by • 0
3
votes
4
replies
8.5k
views
Gene-gene correlation analysis with RNA-seq
edgeR
updated 11 weeks ago by • 0 • written 10.8 years ago by ▴ 30
1
vote
8
replies
521
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 12 weeks ago by 50k • written 12 weeks ago by • 0
4
votes
4
replies
418
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 12 weeks ago by 65k • written 3 months ago by • 0
0
votes
5
replies
594
views
Help with model for differential expression analysis
DifferentialExpression edgeR
3 months ago • updated 12 weeks ago Lucy ▴ 60
6
votes
7
replies
541
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 12 weeks ago by 50k • written 12 weeks ago by • 0
0
votes
0
replies
227
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
3 months ago Jawahar • 0
2
votes
4
replies
541
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
3 months ago Sabiha ▴ 20
0
votes
3
replies
324
views
EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
3
votes
3
replies
644
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
4
votes
9
replies
1.1k
views
RNAseq paired-sample differantial expression analysis with many samples
DESeq2 edgeR
3 months ago Luca • 0
5
votes
7
replies
10.0k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 3 months ago by • 0 • written 7.1 years ago by • 0
0
votes
1
reply
293
views
download problem
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
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 3 months ago by 50k • written 3.0 years ago by ▴ 60
50 results • Page 1 of 1
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Replies
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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