Showing : LIMMA • reset
1
vote
4
replies
137
views
Bulk RNAseq analysis for
DESeq2 RNASeq edgeR limma
1 day ago • updated 13 hours ago Mariami • 0
5
votes
3
replies
604
views
Limma-voom sample weights and impact on DEG numbers
limma
written 7 weeks ago by ▴ 20
4
votes
2
replies
370
views
When to use edgeR or limma
edgeR limma
updated 25 days ago by 53k • written 27 days ago by • 0
0
votes
2
replies
360
views
Combining two proteomics datasets with limpa
limpa ProteomicsWorkflow limma
4 weeks ago • updated 19 days ago Andrew Pattison • 0
0
votes
4
replies
653
views
How does contrasts.fit do in limma to extract comparisons with a model having interaction terms?
limma
updated 5 weeks ago by • 0 • written 7 weeks ago by • 0
0
votes
1
reply
1.3k
views
two questions about limma
Microarray limma Microarray limma
updated 10 weeks ago by 53k • written 18.9 years ago by ▴ 240
2
votes
2
replies
338
views
Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
12 weeks ago • updated 11 weeks ago jamie.gearing ▴ 60
1
vote
2
replies
418
views
Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 6 months ago by ▴ 20
0
votes
1
reply
274
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
1.6k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 4 months ago by 53k • written 5 months ago by • 0
0
votes
4
replies
504
views
voomLmFit fitted log-CPM values
limma edgeR
updated 5 months ago by 53k • written 5 months ago by ▴ 10
1
vote
3
replies
431
views
ROAST compare results with complex design
limma mroast roast CAMERA
written 5 months ago by • 0
2
votes
8
replies
834
views
Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 5 months ago by 53k • written 5 months ago by ▴ 30
3
votes
4
replies
658
views
p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 4 months ago by • 0 • written 5 months ago by • 0
1
vote
2
replies
444
views
Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
6 months ago richardallenfriedmanbrooklyn ▴ 30
3
votes
1
reply
518
views
Limpa Pipeline Order
limma limpa
updated 6 months ago by 53k • written 6 months ago by • 0
3
votes
2
replies
506
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
729
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
6 months ago Jiahao Tian • 0
2
votes
2
replies
493
views
Limma : paired samples leading to unexpected estimates
limma
6 months ago Basti ▴ 780
2
votes
2
replies
642
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
2.1k
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
5.8k
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
7 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
8 months ago Paulito • 0
0
votes
1
reply
530
views
Typo in the help of lmFit()
limma
updated 8 months ago by 53k • written 8 months ago by • 0
0
votes
2
replies
738
views
Limma suqeezeVar
limma
8 months ago Mengchun • 0
0
votes
2
replies
1.5k
views
Limma trend with limpa
limpa limma trend
updated 8 months ago by 53k • written 8 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
9 months ago • updated 4 months ago massimo ▴ 10
0
votes
0
replies
528
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
9 months ago jamiecatalano2 • 0
2
votes
1
reply
787
views
ROAST for small sets
limma mroast
updated 9 months ago by 53k • written 9 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
1.6k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
2
votes
4
replies
1.1k
views
Explanation for ROAST results
CAMERA limma
written 10 months ago by • 0
5
votes
3
replies
1.3k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 10 months ago by 53k • written 10 months ago by ▴ 10
2
votes
2
replies
1.7k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
11 months ago Elizabeth • 0
1
vote
2
replies
1.2k
views
Differential expression of proteins using somascan data
somascan limma
written 11 months ago by • 0
2
votes
4
replies
1.7k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
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
434
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
755
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
883
views
Cross-validation with multiple control subgroups in limma
limma multtest
13 months ago Ali Barry ▴ 40
1
vote
9
replies
1.7k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 14 months ago by ▴ 40
4,231 results • Page 1 of 85
Recent ...
Replies
Comment: Bulk RNAseq analysis for by Mariami • 0
Thank you so much for your help! will try to proceed with the suggestion
Comment: GSEA in R/Bioconductor course by a2a2haa • 0
Academic researchers often share their breakthroughs and course updates through visual stories, making it essential to have tools that pres…
Comment: Bulk RNAseq analysis for by Mariami • 0
Thank you for the explanation. I understand, although at the moment we are limited in our ability to increase N. My concern came from the o…
Answer: Bulk RNAseq analysis for by Gordon Smyth 53k
All three packages allow paired comparisons, where the clone is the "pair". limma moreover allows mixed models (just run `voomLmFit` with `…
Comment: Announcing a New Journal - Bioinformatics Methods and Applications - Now Open fo by a2a2haa • 0
By promoting reproducible analysis, the scientific community can better understand the precise mechanisms that make [Hydrogen inhalation sa…
Votes
Comment: Are transformed values from rlog /vst log2 normalized counts?
Are transformed values from rlog /vst log2 normalized counts?
Answer: Bulk RNAseq analysis for
Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
Awards • All
Popular Question to shepherl 4.3k
Popular Question to Andreas Zankl ▴ 80
Popular Question to Guido Hooiveld ★ 4.1k
Popular Question to Steve Lianoglou ★ 13k
Teacher to Michael Love 43k
Locations • All
Germany, 4 minutes ago
USA, Los Angeles, USC, 49 minutes ago
United States, 52 minutes ago
The city by the bay, 2 hours ago
Melbourne, Australia, 2 hours ago
Traffic: 972 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