Showing : edger • reset
2
votes
3
replies
63
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 4 hours ago by ★ 4.1k • written 6 hours ago by • 0
1
vote
2
replies
200
views
Citation for edgeR user guide
edgeR
written 21 days ago by ▴ 30
1
vote
3
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202
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How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 19 hours ago by 50k • written 1 day ago by • 0
5
votes
3
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298
views
Log-cpm values from limma
limma edgeR RNASeq
updated 5 days ago by 50k • written 27 days ago by • 0
4
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2
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613
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
12 days ago • updated 9 days ago gene_bioconductor ▴ 10
0
votes
1
reply
169
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 12 days ago by 50k • written 13 days ago by • 0
4
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6
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457
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FilterByExpr low counts with small sample size
edgeR
28 days ago • updated 23 days ago Jonathan ▴ 10
3
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3
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362
views
permutation test in edgeR
rna-seq edgeR
updated 24 days ago by 50k • written 5 weeks ago by • 0
6
votes
10
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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
0
votes
3
replies
207
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Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 26 days ago by 50k • written 27 days ago by • 0
0
votes
2
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144
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How to make DGEList and design matrix by edgeR package
DGEList edgeR
26 days ago prity6459 • 0
9
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12
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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
1
vote
3
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364
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Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 4 weeks ago by 50k • written 5 weeks ago by • 0
5
votes
6
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451
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Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 4 weeks ago by ★ 4.1k • written 5 weeks ago by ▴ 30
1
vote
3
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274
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Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 5 weeks ago by 65k • written 5 weeks ago by • 0
0
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2
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190
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
6 weeks ago Marianna ▴ 20
0
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4
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443
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Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
6 weeks ago Lucy ▴ 60
0
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5
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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
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406
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
votes
2
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1.1k
views
library size and fold changes
edgeR edgeR
updated 6 weeks ago by 50k • written 12.4 years ago by ▴ 670
0
votes
6
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366
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Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
5
votes
3
replies
729
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 6 weeks ago by 50k • written 7 weeks ago by ▴ 50
0
votes
1
reply
247
views
Using splicing junction counts with edgeR/limma-voom
splicing limma edgeR
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
2
votes
3
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305
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
2
votes
2
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268
views
between lane normalization upper quantile
EDASeq edgeR
8 weeks ago elesofi • 0
0
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2
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298
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
2
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2
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281
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
8 weeks ago Sabiha ▴ 20
1
vote
3
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435
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
3
votes
4
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483
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
11
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764
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 10 weeks ago by 50k • written 11 weeks ago by • 0
0
votes
1
reply
232
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 10 weeks ago by 50k • written 10 weeks ago by • 0
0
votes
1
reply
274
views
ExactTest vs QLFTest
edgeR
updated 10 weeks ago by 50k • written 11 weeks 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
1
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6
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517
views
Library size normalization in methylation count analysis
edgeR MethylationArray
11 weeks ago mico • 0
5
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4
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418
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
12 weeks ago • updated 11 weeks ago pl23 • 0
0
votes
8
replies
672
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
3 months ago • updated 12 weeks ago Marianna ▴ 20
2
votes
6
replies
432
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
12 weeks ago tsl0026 • 0
3
votes
2
replies
487
views
How does one test for interactions in EdgeR?
edgeR
3 months ago pl23 • 0
1
vote
2
replies
340
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
3 months ago mico • 0
0
votes
4
replies
361
views
Nested paired design
edgeR
3 months ago manduchi ▴ 10
2
votes
3
replies
383
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • written 3 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
1
vote
8
replies
565
views
edgeR error "Design matrix not of full rank"
edgeR methylation
updated 3 months ago by 50k • written 3 months ago by • 0
4
votes
4
replies
448
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
5
replies
637
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
6
votes
7
replies
592
views
readDGE in edgeR giving me path names as sample names
edgeR
updated 3 months ago by 50k • written 3 months ago by • 0
0
votes
0
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257
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
631
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
361
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
699
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
50 results • Page 1 of 1
Recent ...
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Comment: Create protein sequences including variants from a VCF file by Yun • 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization? by Daniel • 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Thanks again Guido, I will try to run the script you have suggested and see if I can install the package. Yes, I have seen this message a…
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Guido Hooiveld ★ 4.0k
FWIW: based on [previous posts][1] it is suggested to install like this: install.packages(pkgs="./org.Vdahliae.eg.db", repos=NULL, typ…
Votes
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
Answer: SGSeq: moving toward diffex from SGSeq analysis
Answer: How to design DEXSeq formula for multiple variables
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