Showing : edger • reset
2
votes
3
replies
66
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 5 hours ago by ★ 4.1k • written 8 hours ago by • 0
1
vote
3
replies
203
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 20 hours ago by 50k • written 1 day ago by • 0
0
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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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2
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613
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
13 days ago • updated 9 days ago gene_bioconductor ▴ 10
1
vote
2
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200
views
Citation for edgeR user guide
edgeR
written 22 days ago by ▴ 30
4
votes
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
0
votes
2
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144
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
26 days ago prity6459 • 0
0
votes
3
replies
207
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 26 days ago by 50k • written 27 days ago by • 0
5
votes
3
replies
299
views
Log-cpm values from limma
limma edgeR RNASeq
updated 5 days ago by 50k • written 27 days ago by • 0
3
votes
3
replies
362
views
permutation test in edgeR
rna-seq edgeR
updated 24 days ago by 50k • written 5 weeks ago by • 0
1
vote
3
replies
364
views
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
replies
452
views
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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275
views
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
votes
2
replies
191
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
6 weeks ago Marianna ▴ 20
0
votes
4
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444
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
6 weeks ago Lucy ▴ 60
3
votes
5
replies
406
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
0
votes
6
replies
367
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 6 weeks ago by 50k • written 6 weeks ago by • 0
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
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
2
votes
3
replies
306
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
0
votes
2
replies
299
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 weeks ago by 50k • written 8 weeks ago by • 0
2
votes
2
replies
269
views
between lane normalization upper quantile
EDASeq edgeR
8 weeks ago elesofi • 0
2
votes
2
replies
282
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
8 weeks ago Sabiha ▴ 20
1
vote
3
replies
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
replies
485
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
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
11
replies
765
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
274
views
ExactTest vs QLFTest
edgeR
updated 10 weeks ago by 50k • written 11 weeks ago by • 0
1
vote
6
replies
518
views
Library size normalization in methylation count analysis
edgeR MethylationArray
11 weeks ago mico • 0
2
votes
6
replies
433
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
12 weeks ago tsl0026 • 0
5
votes
4
replies
419
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
3
votes
2
replies
488
views
How does one test for interactions in EdgeR?
edgeR
3 months ago pl23 • 0
0
votes
4
replies
361
views
Nested paired design
edgeR
3 months ago manduchi ▴ 10
1
vote
2
replies
340
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
3 months ago mico • 0
2
votes
3
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383
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 65k • 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
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
1
vote
8
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565
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
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
632
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
362
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
700
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
4 months ago Luca • 0
0
votes
1
reply
318
views
download problem
edgeR
updated 4 months ago by 50k • 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
1
vote
2
replies
487
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
5
votes
2
replies
594
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 5 months ago by 50k • written 5 months ago by • 0
1
vote
2
replies
449
views
EdgeR: Exact test and glmQLFTest produce very different results
DifferentialExpression edgeR
updated 5 months ago by 50k • written 5 months ago by • 0
7
votes
2
replies
848
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
50 results • Page 1 of 1
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Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Marcel Ramos 690
`BiocManager` does not install local packages. It only installs Bioconductor, CRAN, and GitHub ones. You should install local packages w…
Comment: error running enricher from clusterprofiler by Yael • 0
It worked!!! Thanks alot, i think something in the gene_list wasnt right... Thanks agian
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`. …
Votes
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Answer: Trim/Filter out-of-bounds GRanges
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
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