Showing : edger • reset
2
votes
3
replies
141
views
How to correctly adjust for gender in edgeR
design glm edgeR
updated 5 days ago by 50k • written 5 days ago by • 0
1
vote
3
replies
260
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 6 days ago by 50k • written 7 days ago by • 0
0
votes
1
reply
180
views
NEED FOR NESSASORY HELP
RNASeqData edgeR
updated 18 days ago by 50k • written 18 days ago by • 0
4
votes
2
replies
639
views
Why does GSEA on edgeR results for randomized samples give highly significant p-values?
fgsea edgeR
18 days ago • updated 14 days ago gene_bioconductor ▴ 10
1
vote
2
replies
207
views
Citation for edgeR user guide
edgeR
written 27 days ago by ▴ 30
4
votes
6
replies
475
views
FilterByExpr low counts with small sample size
edgeR
4 weeks ago • updated 28 days ago Jonathan ▴ 10
0
votes
2
replies
151
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
320
views
Log-cpm values from limma
limma edgeR RNASeq
updated 10 days ago by 50k • written 4 weeks ago by • 0
3
votes
3
replies
370
views
permutation test in edgeR
rna-seq edgeR
updated 29 days ago by 50k • written 6 weeks ago by • 0
1
vote
3
replies
369
views
Why is my gene not significantly differentially expressed?
limmaGUI edgeR limma
updated 5 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
284
views
Lib sizes in the DGE object are different from original lib sizes
edgeR DifferentialExpression
updated 6 weeks ago by 66k • written 6 weeks ago by • 0
0
votes
2
replies
201
views
edgeR analysis: glm functions and offset matrix
tximport edgeR Normalization
6 weeks ago Marianna ▴ 20
0
votes
4
replies
449
views
Adjust RNA-seq counts (more than one batch variable) for plotting differentially expressed genes
ComBat sva edgeR
7 weeks ago • updated 6 weeks ago Lucy ▴ 60
3
votes
5
replies
416
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
377
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
256
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
744
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
313
views
edgeR, 3 x 2 design with a batch effect and contrasts
design edgeR contrasts
updated 8 weeks ago by 50k • written 9 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
276
views
between lane normalization upper quantile
EDASeq edgeR
9 weeks ago elesofi • 0
2
votes
2
replies
291
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
443
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
523
views
Right way to pseudobulk donors across replicates in edgeR
pseudobulk edgeR DifferentialExpression
updated 10 weeks ago by 50k • written 11 weeks ago by ▴ 50
0
votes
1
reply
244
views
Different results from DGE using different subgroups in model.matrix
edgeR
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
0
votes
11
replies
799
views
Strange logFC values in differential methylation site anslysis
edgeR MethylationArray
updated 11 weeks ago by 50k • written 12 weeks ago by • 0
0
votes
1
reply
290
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
12 weeks ago mico • 0
2
votes
6
replies
445
views
edgeR: DEGs in a CRD factorial (2x2x2)
edgeR
3 months ago tsl0026 • 0
5
votes
4
replies
434
views
Confusion about LFC using contrasts weights in EdgeR
edgeR
3 months ago • updated 12 weeks ago pl23 • 0
0
votes
8
replies
690
views
Divergent results using exact, glmLRT, and glmQLF tests in edgeR
edgeR
3 months ago Marianna ▴ 20
3
votes
2
replies
507
views
How does one test for interactions in EdgeR?
edgeR
3 months ago pl23 • 0
0
votes
4
replies
369
views
Nested paired design
edgeR
3 months ago manduchi ▴ 10
1
vote
2
replies
354
views
How to get normalized values for methylation counts in edgeR
edgeR MethylationArray
3 months ago mico • 0
2
votes
3
replies
392
views
TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 3 months ago by 66k • written 3 months ago by • 0
4
votes
4
replies
462
views
edgeR - Design matrix for comparisons of all and subsets of samples
edgeR
updated 3 months ago by 66k • written 4 months ago by • 0
6
votes
7
replies
613
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
584
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
270
views
Which normalization should I do use for ATAC Seq using DiffBind
DiffBind edgeR ATACSeq DESeq2
4 months ago Jawahar • 0
2
votes
4
replies
653
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago Sabiha ▴ 20
0
votes
3
replies
389
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
728
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
327
views
download problem
edgeR
updated 4 months ago by 50k • written 4 months ago by • 0
0
votes
5
replies
646
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 Sabiha ▴ 20
5
votes
2
replies
607
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
465
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
868
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: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k
If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …
Comment: Help with ENmix readidat by James W. MacDonald 66k
Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …
Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 66k
In that case, probably easiest to subset to the groups being compared.
Comment: Help with ENmix readidat by minardsmitha ▴ 10
Did you figure this out? I have the same issue.
Comment: LRT, more than two conditions and pairwise comparisons by boczniak767 ▴ 720
Thank you for response, apparently I still don't know much about statistics. In fact I want to campare time-profiles [and the LRT has been …
Votes
Answer: Control group between 2 batches have different expression in RNAseq data
Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?
Comment: DESeq2- Mysterious interaction suppresses DEGs
Answer: DESeq2- Mysterious interaction suppresses DEGs
Answer: Subsetting RNAseq data | voomaByGroup()
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