Showing : limma • reset
0
votes
2
replies
150
views
Can sample-level weights be used when analysing GSVA scores in limma?
limma
updated 4 days ago by ★ 3.4k • written 5 days ago by ▴ 20
1
vote
4
replies
331
views
Bulk RNAseq analysis for
DESeq2 RNASeq edgeR limma
14 days ago • updated 13 days ago Mariami • 0
5
votes
3
replies
705
views
Limma-voom sample weights and impact on DEG numbers
limma
written 8 weeks ago by ▴ 20
4
votes
2
replies
468
views
When to use edgeR or limma
edgeR limma
updated 5 weeks ago by 53k • written 5 weeks ago by • 0
0
votes
2
replies
433
views
Combining two proteomics datasets with limpa
limpa ProteomicsWorkflow limma
6 weeks ago • updated 4 weeks ago Andrew Pattison • 0
0
votes
4
replies
690
views
How does contrasts.fit do in limma to extract comparisons with a model having interaction terms?
limma
updated 7 weeks ago by • 0 • written 9 weeks ago by • 0
0
votes
1
reply
1.3k
views
two questions about limma
Microarray limma Microarray limma
updated 12 weeks ago by 53k • written 19.0 years ago by ▴ 240
2
votes
2
replies
360
views
Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
3 months ago jamie.gearing ▴ 60
1
vote
2
replies
438
views
Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 6 months ago by ▴ 20
0
votes
1
reply
290
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 4 months ago by 53k • written 4 months ago by • 0
5
votes
13
replies
1.7k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 5 months ago by 53k • written 5 months ago by • 0
0
votes
4
replies
532
views
voomLmFit fitted log-CPM values
limma edgeR
updated 5 months ago by 53k • written 5 months ago by ▴ 10
1
vote
3
replies
451
views
ROAST compare results with complex design
limma mroast roast CAMERA
written 5 months ago by • 0
2
votes
8
replies
848
views
Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 5 months ago by 53k • written 6 months ago by ▴ 30
3
votes
4
replies
676
views
p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 5 months ago by • 0 • written 6 months ago by • 0
1
vote
2
replies
458
views
Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
6 months ago richardallenfriedmanbrooklyn ▴ 30
3
votes
1
reply
549
views
Limpa Pipeline Order
limma limpa
updated 6 months ago by 53k • written 6 months ago by • 0
3
votes
2
replies
518
views
Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 6 months ago by 53k • written 6 months ago by ▴ 20
0
votes
8
replies
756
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
6 months ago Jiahao Tian • 0
2
votes
2
replies
513
views
Limma : paired samples leading to unexpected estimates
limma
6 months ago Basti ▴ 780
2
votes
2
replies
663
views
(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
6 months ago sandmann.t ▴ 70
4
votes
8
replies
2.2k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
7 months ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
replies
5.9k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
7 months ago bbao ▴ 10
0
votes
1
reply
1.5k
views
How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray limma BRAIN Microarray limma BRAIN
updated 7 months ago by 53k • written 17.0 years ago by ▴ 10
0
votes
3
replies
2.6k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma Bioconductor Metabolomics
updated 7 months ago by 53k • written 7 months ago by • 0
0
votes
4
replies
1.9k
views
How to use goana function with zebrafish genome from org.Dr.eg.db
org.Dr.eg.db zebrafish limma
8 months ago Eric • 0
3
votes
2
replies
6.5k
views
limma duplicateCorrelation appropriate where some blocks cross condition and some are in same condition?
limma
8 months ago Geoff • 0
2
votes
3
replies
1.7k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
9 months ago Paulito • 0
0
votes
1
reply
535
views
Typo in the help of lmFit()
limma
updated 9 months ago by 53k • written 9 months ago by • 0
0
votes
2
replies
752
views
Limma suqeezeVar
limma
9 months ago Mengchun • 0
0
votes
2
replies
1.6k
views
Limma trend with limpa
limpa limma trend
updated 9 months ago by 53k • written 9 months ago by • 0
2
votes
5
replies
1.4k
views
Dealing with heteroscedascity in limma
limma splines Proteomics
written 9 months ago by • 0
5
votes
7
replies
3.6k
views
limma correction for tumor purity
limma
9 months ago gabriella.jacobson-eisenberg ▴ 20
0
votes
3
replies
1.2k
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 10 months ago by ▴ 10
4
votes
7
replies
3.6k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
10 months ago • updated 4 months ago massimo ▴ 10
0
votes
0
replies
537
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
10 months ago jamiecatalano2 • 0
2
votes
1
reply
796
views
ROAST for small sets
limma mroast
updated 10 months ago by 53k • written 10 months ago by • 0
2
votes
4
replies
2.0k
views
how to use `arrayWeightsQuick()`?
limma
updated 9 months ago by • 0 • written 10 months ago by • 0
2
votes
2
replies
1.7k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 11 months ago by ★ 5.0k • written 11 months ago by • 0
2
votes
4
replies
1.1k
views
Explanation for ROAST results
CAMERA limma
written 11 months ago by • 0
5
votes
3
replies
1.4k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 11 months ago by 53k • written 11 months ago by ▴ 10
2
votes
2
replies
1.8k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
11 months ago Elizabeth • 0
1
vote
2
replies
1.3k
views
Differential expression of proteins using somascan data
somascan limma
written 11 months ago by • 0
2
votes
4
replies
1.8k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
12 months ago • updated 11 months ago svlachavas ▴ 840
3
votes
5
replies
2.5k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 13 months ago by 68k • written 13 months ago by ▴ 10
0
votes
0
replies
442
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
13 months ago GJ • 0
0
votes
2
replies
768
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 13 months ago by ▴ 840
2
votes
5
replies
1.0k
views
Differential variability modelling with vst() expression
limma DESeq2
written 13 months ago by • 0
6
votes
5
replies
1.2k
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 13 months ago by 68k • written 13 months ago by • 0
0
votes
2
replies
902
views
Cross-validation with multiple control subgroups in limma
limma multtest
14 months ago Ali Barry ▴ 40
4,232 results • Page 1 of 85
Recent ...
Replies
Comment: Question on processing compound protein groups in limpa by JKim • 0
Many thanks. I appreciate your advice.
Answer: Question on processing compound protein groups in limpa by Gordon Smyth 53k
Different people have different ways of dealing with compound protein groups. You could just leave them in the analysis, in which case limp…
Answer: Correct usage of limpa for protein input by Gordon Smyth 53k
limpa can work on protein-level quantifications, but they must be intensity-based and must be on the log scale. From what I read (<https://…
Comment: A problem occurs when running the monocle2 by a2a2hset32aa • 0
Troubleshooting monocle2 errors in R 4.5.1 often points to package incompatibilities, particularly with newer versions of igraph. For resea…
Comment: Deadline Extended: EuroBioC2026 Call for Abstracts by a2a2hset32aa • 0
Attending EuroBioC2026 is an excellent way for researchers to explore the intersection of technology and biology. For those seeking high qu…
Votes
Answer: Question on processing compound protein groups in limpa
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
Answer: Correct usage of limpa for protein input
A: Interpretaion of dendrogram height in WGCNA?
Awards • All
Popular Question to Dario Strbenac ★ 1.6k
Popular Question to chirag.parsania ▴ 10
Popular Question to Michael Love 43k
Popular Question to Dan Tenenbaum ★ 8.2k
Scholar to Gordon Smyth 53k
Locations • All
United States, 3 minutes ago
United States, 22 minutes ago
Melbourne, Australia, 57 minutes ago
United States, 1 hour ago
United States, 1 hour ago
Traffic: 1182 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