Showing : EdgeR • reset
2
votes
3
replies
122
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 3 days ago by 50k • written 4 days ago by • 0
1
vote
3
replies
246
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 4 days ago by 50k • written 5 days ago by • 0
0
votes
1
reply
177
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 16 days ago by 50k • written 16 days ago by • 0
4
votes
2
replies
627
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
16 days ago • updated 12 days ago gene_bioconductor ▴ 10
1
vote
2
replies
204
views
Citation for edgeR user guide
edgeR
written 25 days ago by ▴ 30
4
votes
6
replies
472
views
FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 26 days ago Jonathan ▴ 10
0
votes
2
replies
150
views
How to make DGEList and design matrix by edgeR package
DGEList edgeR
4 weeks ago prity6459 • 0
0
votes
3
replies
217
views
Finding DEGs by using edgeR
subsettingdata edgeR designmatrix
updated 4 weeks ago by 50k • written 4 weeks ago by • 0
5
votes
3
replies
311
views
Log-cpm values from limma
limma edgeR RNASeq
updated 9 days ago by 50k • written 4 weeks ago by • 0
3
votes
3
replies
368
views
permutation test in edgeR
rna-seq edgeR
updated 28 days ago by 50k • written 5 weeks ago by • 0
1
vote
3
replies
369
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
462
views
Not fully paired differential gene expression analysis
edgeR DifferentialExpression
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by ▴ 30
1
vote
3
replies
280
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 6 weeks ago by 65k • written 6 weeks ago by • 0
0
votes
2
replies
198
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
6 weeks ago Marianna ▴ 20
0
votes
4
replies
448
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
414
views
Differing results from plotMDS and PCAtools
edgeR PCAtools
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
0
votes
6
replies
373
views
Doing comparison of RNA-seq data using EdgeR
metaMSdata edgeR
updated 7 weeks ago by 50k • written 7 weeks ago by • 0
0
votes
1
reply
252
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
739
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
311
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
305
views
RNAseq analysis
rnaseqGene edgeR DEGraph DifferentialExpression
updated 9 weeks ago by 50k • written 9 weeks ago by • 0
2
votes
2
replies
275
views
between lane normalization upper quantile
EDASeq edgeR
9 weeks ago • updated 8 weeks ago elesofi • 0
2
votes
2
replies
289
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
9 weeks ago Sabiha ▴ 20
1
vote
3
replies
440
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
509
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
242
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
796
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
287
views
ExactTest vs QLFTest
edgeR
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
1
vote
6
replies
528
views
Library size normalization in methylation count analysis
edgeR MethylationArray
11 weeks ago mico • 0
2
votes
6
replies
443
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
3 months ago tsl0026 • 0
5
votes
4
replies
430
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
3 months ago • updated 12 weeks ago pl23 • 0
0
votes
8
replies
684
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
504
views
How does one test for interactions in EdgeR?
edgeR
3 months ago pl23 • 0
0
votes
4
replies
367
views
Nested paired design
edgeR
3 months ago manduchi ▴ 10
1
vote
2
replies
351
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
3 months ago mico • 0
2
votes
3
replies
388
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
457
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
608
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
581
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
268
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
650
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
383
views
EdgeR for methylation analysis when there is no replicates
RRBSdata edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
3
votes
3
replies
719
views
EdgeR: Should I include all samples/conditions in my dispersion estimation while only testing for certain contrasts
edgeR
updated 4 months ago by 50k • 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
326
views
download problem
edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
0
votes
5
replies
644
views
Help with model for differential expression analysis
DifferentialExpression edgeR
4 months ago • updated 3 months ago Lucy ▴ 60
1
vote
2
replies
498
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
5 months ago • updated 4 months ago Sabiha ▴ 20
5
votes
2
replies
602
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
460
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
864
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 ...
Replies
Answer: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
Your code is poorly readable. Suggest you select and then highlight with markdown using the `10101` button. Generally, colData(dds) must…
Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
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: 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!
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
Awards • All
Popular Question to Dario Strbenac ★ 1.5k
Popular Question to Vincent J. Carey, Jr. 6.7k
Popular Question to Koen Van den Berge ▴ 180
Popular Question to shepherl 3.9k
Popular Question to Ken C • 0
Locations • All
Hong Kong, just now
Germany, 44 minutes ago
Slovakia, 58 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
Pakistan, 1 hour ago
Traffic: 408 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6