Showing : Limma • reset
0
votes
1
reply
1.1k
views
two questions about limma
Microarray limma Microarray limma
updated 5 hours ago by 53k • written 18.7 years ago by ▴ 240
2
votes
2
replies
231
views
Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
11 days ago • updated 10 days ago jamie.gearing ▴ 60
1
vote
2
replies
332
views
Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 3 months ago by ▴ 10
0
votes
1
reply
201
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 7 weeks ago by 53k • written 8 weeks ago by • 0
5
votes
13
replies
1.2k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 9 weeks ago by 53k • written 11 weeks ago by • 0
0
votes
4
replies
419
views
voomLmFit fitted log-CPM values
limma edgeR
updated 12 weeks ago by 53k • written 12 weeks ago by ▴ 10
1
vote
3
replies
357
views
ROAST compare results with complex design
limma mroast roast CAMERA
written 12 weeks ago by • 0
2
votes
8
replies
718
views
Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 12 weeks ago by 53k • written 3 months ago by ▴ 30
3
votes
4
replies
502
views
p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 10 weeks ago by • 0 • written 3 months ago by • 0
1
vote
2
replies
357
views
Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
3 months ago richardallenfriedmanbrooklyn ▴ 30
3
votes
1
reply
354
views
Limpa Pipeline Order
limma limpa
updated 3 months ago by 53k • written 3 months ago by • 0
3
votes
2
replies
436
views
Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 3 months ago by 53k • written 3 months ago by ▴ 10
0
votes
8
replies
621
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
3 months ago Jiahao Tian • 0
2
votes
2
replies
409
views
Limma : paired samples leading to unexpected estimates
limma
4 months ago Basti ▴ 780
2
votes
2
replies
504
views
(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
4 months ago sandmann.t ▴ 70
4
votes
8
replies
1.9k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
4 months ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
replies
5.6k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
4 months ago bbao ▴ 10
0
votes
1
reply
1.4k
views
How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray limma BRAIN Microarray limma BRAIN
updated 4 months ago by 53k • written 16.8 years ago by ▴ 10
0
votes
3
replies
2.3k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma Bioconductor Metabolomics
updated 4 months ago by 53k • written 5 months ago by • 0
0
votes
4
replies
1.8k
views
How to use goana function with zebrafish genome from org.Dr.eg.db
org.Dr.eg.db zebrafish limma
5 months ago Eric • 0
3
votes
2
replies
6.4k
views
limma duplicateCorrelation appropriate where some blocks cross condition and some are in same condition?
limma
6 months ago Geoff • 0
2
votes
3
replies
1.5k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
6 months ago Paulito • 0
0
votes
1
reply
476
views
Typo in the help of lmFit()
limma
updated 6 months ago by 53k • written 6 months ago by • 0
0
votes
2
replies
660
views
Limma suqeezeVar
limma
6 months ago Mengchun • 0
0
votes
2
replies
1.3k
views
Limma trend with limpa
limpa limma trend
updated 6 months ago by 53k • written 6 months ago by • 0
2
votes
5
replies
1.2k
views
Dealing with heteroscedascity in limma
limma splines Proteomics
written 6 months ago by • 0
5
votes
7
replies
3.3k
views
limma correction for tumor purity
limma
6 months ago gabriella.jacobson-eisenberg ▴ 20
0
votes
3
replies
986
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 7 months ago by ▴ 10
4
votes
7
replies
3.3k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
7 months ago • updated 7 weeks ago massimo ▴ 10
0
votes
0
replies
452
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
7 months ago jamiecatalano2 • 0
2
votes
1
reply
688
views
ROAST for small sets
limma mroast
updated 7 months ago by 53k • written 7 months ago by • 0
2
votes
4
replies
1.9k
views
how to use `arrayWeightsQuick()`?
limma
updated 6 months ago by • 0 • written 7 months ago by • 0
2
votes
2
replies
1.5k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 8 months ago by ★ 5.0k • written 8 months ago by • 0
2
votes
4
replies
975
views
Explanation for ROAST results
CAMERA limma
written 8 months ago by • 0
5
votes
3
replies
1.2k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 8 months ago by 53k • written 8 months ago by ▴ 10
2
votes
2
replies
1.6k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
8 months ago Elizabeth • 0
1
vote
2
replies
1.1k
views
Differential expression of proteins using somascan data
somascan limma
written 8 months ago by • 0
2
votes
4
replies
1.5k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
9 months ago svlachavas ▴ 840
3
votes
5
replies
2.1k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 10 months ago by 68k • written 10 months ago by ▴ 10
0
votes
0
replies
380
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
10 months ago GJ • 0
0
votes
2
replies
668
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 10 months ago by ▴ 840
2
votes
5
replies
796
views
Differential variability modelling with vst() expression
limma DESeq2
written 10 months ago by • 0
6
votes
5
replies
1.1k
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 10 months ago by 68k • written 11 months ago by • 0
0
votes
2
replies
793
views
Cross-validation with multiple control subgroups in limma
limma multtest
11 months ago Ali Barry ▴ 40
1
vote
9
replies
1.5k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 11 months ago by ▴ 40
0
votes
2
replies
710
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
11 months ago Tadeoye ▴ 20
0
votes
2
replies
916
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 11 months ago by 53k • written 11 months ago by ▴ 10
2
votes
3
replies
1.8k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 11 months ago by 68k • written 12 months ago by ▴ 10
1
vote
2
replies
722
views
contrast matrix design for a continuous variable
limma
12 months ago • updated 10 months ago dtzhu337 • 0
3
votes
3
replies
1.0k
views
Crossover design with limma
limma crossover
updated 11 months ago by 53k • written 12 months ago by ▴ 30
4,226 results • Page 1 of 85
Recent ...
Replies
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to shepherl 4.2k
Popular Question to Gordon Smyth 53k
Popular Question to k___ ▴ 30
Popular Question to efoss ▴ 10
Popular Question to James W. MacDonald 68k
Locations • All
The city by the bay, 19 minutes ago
United States, 49 minutes ago
United States, 51 minutes ago
United States, 56 minutes ago
United States, 2 hours ago
Traffic: 746 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