Showing : Limma • reset
0
votes
1
reply
1.2k
views
two questions about limma
Microarray limma Microarray limma
updated 17 days ago by 53k • written 18.8 years ago by ▴ 240
2
votes
2
replies
266
views
Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
28 days ago • updated 27 days ago jamie.gearing ▴ 60
1
vote
2
replies
354
views
Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 4 months ago by ▴ 10
0
votes
1
reply
220
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 10 weeks ago by 53k • written 10 weeks ago by • 0
5
votes
13
replies
1.3k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 12 weeks ago by 53k • written 3 months ago by • 0
0
votes
4
replies
438
views
voomLmFit fitted log-CPM values
limma edgeR
updated 3 months ago by 53k • written 3 months ago by ▴ 10
1
vote
3
replies
377
views
ROAST compare results with complex design
limma mroast roast CAMERA
written 3 months ago by • 0
2
votes
8
replies
750
views
Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 3 months ago by 53k • written 4 months ago by ▴ 30
3
votes
4
replies
538
views
p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 3 months ago by • 0 • written 4 months ago by • 0
1
vote
2
replies
389
views
Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
4 months ago richardallenfriedmanbrooklyn ▴ 30
3
votes
1
reply
387
views
Limpa Pipeline Order
limma limpa
updated 4 months ago by 53k • written 4 months ago by • 0
3
votes
2
replies
457
views
Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 4 months ago by 53k • written 4 months ago by ▴ 10
0
votes
8
replies
654
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
4 months ago Jiahao Tian • 0
2
votes
2
replies
427
views
Limma : paired samples leading to unexpected estimates
limma
4 months ago Basti ▴ 780
2
votes
2
replies
524
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
5 months ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
replies
5.7k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
5 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 5 months ago by 53k • written 16.9 years ago by ▴ 10
0
votes
3
replies
2.4k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma Bioconductor Metabolomics
updated 5 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
6 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
490
views
Typo in the help of lmFit()
limma
updated 7 months ago by 53k • written 7 months ago by • 0
0
votes
2
replies
675
views
Limma suqeezeVar
limma
7 months ago • updated 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 7 months ago by • 0
2
votes
5
replies
1.3k
views
Dealing with heteroscedascity in limma
limma splines Proteomics
written 7 months ago by • 0
5
votes
7
replies
3.4k
views
limma correction for tumor purity
limma
7 months ago gabriella.jacobson-eisenberg ▴ 20
0
votes
3
replies
1.0k
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 8 months ago by ▴ 10
4
votes
7
replies
3.3k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
7 months ago • updated 10 weeks ago massimo ▴ 10
0
votes
0
replies
470
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
713
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 7 months ago by • 0 • written 8 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
1.0k
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 9 months ago by 53k • written 9 months ago by ▴ 10
2
votes
2
replies
1.6k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
9 months ago Elizabeth • 0
1
vote
2
replies
1.1k
views
Differential expression of proteins using somascan data
somascan limma
written 9 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
10 months ago • updated 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 11 months ago by 68k • written 11 months ago by ▴ 10
0
votes
0
replies
389
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
11 months ago GJ • 0
0
votes
2
replies
685
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 11 months ago by ▴ 840
2
votes
5
replies
828
views
Differential variability modelling with vst() expression
limma DESeq2
written 11 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 11 months ago by 68k • written 11 months ago by • 0
0
votes
2
replies
807
views
Cross-validation with multiple control subgroups in limma
limma multtest
12 months ago Ali Barry ▴ 40
1
vote
9
replies
1.6k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 12 months ago by ▴ 40
0
votes
2
replies
727
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
12 months ago Tadeoye ▴ 20
0
votes
2
replies
941
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 12 months ago by 53k • written 12 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 12 months ago by 68k • written 12 months ago by ▴ 10
1
vote
2
replies
736
views
contrast matrix design for a continuous variable
limma
12 months ago • updated 11 months ago dtzhu337 • 0
3
votes
3
replies
1.1k
views
Crossover design with limma
limma crossover
updated 12 months ago by 53k • written 12 months ago by ▴ 30
4,226 results • Page 1 of 85
Recent ...
Replies
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
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
Awards • All
Popular Question to lamia11me • 0
Popular Question to Gordon Smyth 53k
Popular Question to Michael Love 43k
Popular Question to Luca • 0
Popular Question to Lluís Revilla Sancho ▴ 760
Locations • All
United States, 45 minutes ago
Melbourne, Australia, 1 hour ago
United States, 1 hour ago
United Kingdom, 1 hour ago
The city by the bay, 2 hours ago
Traffic: 2299 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