Showing : edger • reset
2
votes
3
replies
107
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 1 day ago by 50k • written 2 days ago by • 0
1
vote
3
replies
220
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 2 days ago by 50k • written 3 days ago by • 0
4
votes
2
replies
619
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
14 days ago • updated 10 days ago gene_bioconductor ▴ 10
0
votes
1
reply
172
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 14 days ago by 50k • written 14 days ago by • 0
1
vote
2
replies
201
views
Citation for edgeR user guide
edgeR
written 23 days ago by ▴ 30
0
votes
2
replies
146
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
28 days ago prity6459 • 0
0
votes
3
replies
209
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 28 days ago by 50k • written 28 days ago by • 0
5
votes
3
replies
304
views
Log-cpm values from limma
limma edgeR RNASeq
updated 7 days ago by 50k • written 29 days ago by • 0
4
votes
6
replies
464
views
FilterByExpr low counts with small sample size
edgeR
29 days ago • updated 25 days ago Jonathan ▴ 10
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
5
votes
6
replies
456
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 4 weeks ago by ★ 4.1k • written 5 weeks ago by ▴ 30
3
votes
3
replies
366
views
permutation test in edgeR
rna-seq edgeR
updated 26 days ago by 50k • written 5 weeks ago by • 0
1
vote
3
replies
278
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 5 weeks ago by 65k • written 6 weeks ago by • 0
0
votes
2
replies
195
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
6 weeks ago Marianna ▴ 20
0
votes
4
replies
447
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
412
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 6 weeks ago by 50k • written 7 weeks ago by • 0
0
votes
6
replies
370
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 6 weeks ago by 50k • written 7 weeks ago by • 0
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
5
votes
3
replies
734
views
What benchmark should I use for setting the EdgeR filterByExpr min.count parameter?
edgeR DifferentialExpression
updated 7 weeks ago by 50k • written 8 weeks ago by ▴ 50
2
votes
3
replies
309
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
303
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 8 weeks ago by 50k • written 9 weeks ago by • 0
2
votes
2
replies
273
views
between lane normalization upper quantile
EDASeq edgeR
9 weeks ago • updated 8 weeks ago elesofi • 0
2
votes
2
replies
288
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 weeks ago Sabiha ▴ 20
3
votes
4
replies
502
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
239
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
280
views
ExactTest vs QLFTest
edgeR
updated 10 weeks ago by 50k • written 11 weeks ago by • 0
0
votes
11
replies
778
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 10 weeks ago by 50k • written 11 weeks ago by • 0
1
vote
6
replies
525
views
Library size normalization in methylation count analysis
edgeR MethylationArray
11 weeks ago mico • 0
5
votes
4
replies
425
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
3 months ago • updated 12 weeks ago pl23 • 0
2
votes
6
replies
437
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
3 months ago • updated 12 weeks ago tsl0026 • 0
0
votes
8
replies
678
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
494
views
How does one test for interactions in EdgeR?
edgeR
3 months ago pl23 • 0
0
votes
4
replies
364
views
Nested paired design
edgeR
3 months ago manduchi ▴ 10
1
vote
2
replies
348
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
3 months ago mico • 0
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
1
vote
3
replies
437
views
Cross-species analysis - how to compute the mid parent value?
DESeq2 limma edgeR DifferentialExpression
written 3 months ago by • 0
6
votes
7
replies
599
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
replies
571
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
replies
266
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
645
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
378
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
709
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 4 months ago by • 0
4
votes
4
replies
455
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
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
324
views
download problem
edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
0
votes
5
replies
641
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
1
vote
2
replies
492
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
4 months ago Sabiha ▴ 20
5
votes
2
replies
599
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
455
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
859
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
Recent ...
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Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
ok. Forcing non-secure protocol should not be needed anymore, due to changes in the underlying library. However, I will look at why "HTTP" …
Comment: STRINGdb : error with string_db$plot_network() by ninidea • 0
> Does the vignette produce the same error? No. Anyway, I finally solved the problem. I don't know why, but I removed: protocol='http' fr…
Comment: maSigPro genes from clusters by anne-laure • 0
Hello It is a litlle bit late but I do not get how to extract the genes from each cluster identified by see.genes(sigs$sig.genes$Day4vs…
Comment: STRINGdb : error with string_db$plot_network() by damian.szk ▴ 80
Your code seems ok. Does the vignette produce the same error? [link to STRINGdb R script vignette][1] [1]: https://www.bioconductor.or…
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
Hi @marcelramos Thanks for the clarification. Yes, I have installed `org.Vdahlaie.eg.db` using the code you and Guido suggested and now i…
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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