Showing : Limma • reset
0
votes
1
reply
78
views
specifying refColumn in calcNormFactors()
edgeR limma
updated 23 hours ago by 53k • written 2 days ago by • 0
5
votes
3
replies
905
views
Limma-voom sample weights and impact on DEG numbers
limma
written 11 weeks ago by ▴ 20
3
votes
3
replies
334
views
Can sample-level weights be used when analysing GSVA scores in limma?
limma
23 days ago • updated 16 days ago A.Barden ▴ 20
1
vote
4
replies
469
views
Bulk RNAseq analysis for
DESeq2 RNASeq edgeR limma
4 weeks ago Mariami • 0
4
votes
2
replies
686
views
When to use edgeR or limma
edgeR limma
updated 8 weeks ago by 53k • written 8 weeks ago by • 0
0
votes
2
replies
522
views
Combining two proteomics datasets with limpa
limpa ProteomicsWorkflow limma
9 weeks ago • updated 7 weeks ago Andrew Pattison • 0
0
votes
4
replies
747
views
How does contrasts.fit do in limma to extract comparisons with a model having interaction terms?
limma
updated 9 weeks ago by • 0 • written 12 weeks ago by • 0
0
votes
1
reply
1.4k
views
two questions about limma
Microarray limma Microarray limma
updated 3 months ago by 53k • written 19.0 years ago by ▴ 240
2
votes
2
replies
407
views
Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
3 months ago jamie.gearing ▴ 60
1
vote
2
replies
484
views
Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 7 months ago by ▴ 20
0
votes
1
reply
324
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 5 months ago by 53k • written 5 months ago by • 0
5
votes
13
replies
2.0k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 5 months ago by 53k • written 6 months ago by • 0
0
votes
4
replies
595
views
voomLmFit fitted log-CPM values
limma edgeR
updated 6 months ago by 53k • written 6 months ago by ▴ 10
1
vote
3
replies
488
views
ROAST compare results with complex design
limma mroast roast CAMERA
written 6 months ago by • 0
2
votes
8
replies
879
views
Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 6 months ago by 53k • written 7 months ago by ▴ 30
3
votes
4
replies
751
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
479
views
Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
7 months ago richardallenfriedmanbrooklyn ▴ 30
3
votes
1
reply
630
views
Limpa Pipeline Order
limma limpa
updated 7 months ago by 53k • written 7 months ago by • 0
3
votes
2
replies
563
views
Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 7 months ago by 53k • written 7 months ago by ▴ 20
0
votes
8
replies
795
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
7 months ago Jiahao Tian • 0
2
votes
2
replies
554
views
Limma : paired samples leading to unexpected estimates
limma
7 months ago Basti ▴ 780
2
votes
2
replies
692
views
(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
7 months ago sandmann.t ▴ 70
4
votes
8
replies
2.3k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
8 months ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
replies
6.0k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
8 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 8 months ago by 53k • written 17.1 years ago by ▴ 10
0
votes
3
replies
2.7k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma Bioconductor Metabolomics
updated 8 months ago by 53k • written 8 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
9 months ago • updated 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
9 months ago Geoff • 0
2
votes
3
replies
1.8k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
9 months ago Paulito • 0
0
votes
1
reply
556
views
Typo in the help of lmFit()
limma
updated 9 months ago by 53k • written 9 months ago by • 0
0
votes
2
replies
773
views
Limma suqeezeVar
limma
9 months ago Mengchun • 0
0
votes
2
replies
1.7k
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 10 months ago by • 0
5
votes
7
replies
3.6k
views
limma correction for tumor purity
limma
10 months ago gabriella.jacobson-eisenberg ▴ 20
0
votes
3
replies
1.3k
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 11 months ago by ▴ 10
4
votes
7
replies
3.7k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
10 months ago • updated 5 months ago massimo ▴ 10
0
votes
0
replies
552
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
818
views
ROAST for small sets
limma mroast
updated 10 months ago by 53k • written 10 months ago by • 0
2
votes
4
replies
2.1k
views
how to use `arrayWeightsQuick()`?
limma
updated 10 months ago by • 0 • written 11 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 12 months ago by ▴ 10
2
votes
2
replies
1.8k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
12 months ago Elizabeth • 0
1
vote
2
replies
1.3k
views
Differential expression of proteins using somascan data
somascan limma
written 12 months ago by • 0
2
votes
4
replies
1.9k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
12 months ago svlachavas ▴ 840
3
votes
5
replies
2.8k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 14 months ago by 68k • written 14 months ago by ▴ 10
0
votes
0
replies
453
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
14 months ago GJ • 0
0
votes
2
replies
784
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 14 months ago by ▴ 840
2
votes
5
replies
1.1k
views
Differential variability modelling with vst() expression
limma DESeq2
written 14 months ago by • 0
6
votes
5
replies
1.3k
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 14 months ago by 68k • written 14 months ago by • 0
4,233 results • Page 1 of 85
Recent ...
Replies
Answer: Is it still possible to do batch correction for my data? by Gordon Smyth 53k
I agree with the comments from James MacDonald, but I will add that if you use the standard linear model correction for batch ``` design <-…
Answer: specifying refColumn in calcNormFactors() by Gordon Smyth 53k
Your question is about cross-validation rather than specifically about edgeR. A general principle of cross-validation is that you must norm…
Answer: Sex prediction in sesame for EPICV2 by Tim Peters ▴ 230
Hi Pooja, There is a tutorial for preprocessing EPICv2 via sesame here: https://clark-lab.github.io/EPICv2_tutorial/. There is no call t…
Comment: Convergence Issues and Model Selection DESeq2 by dani.guan.3 • 0
Thank you, I appreciate your time and help.
Comment: Convergence Issues and Model Selection DESeq2 by Michael Love 43k
> out of my 30,229 genes, 795 (2.6%) are better explained ... Not exactly. Frequentist statistics is not symmetric in this way. If it were…
Votes
DiffBind dropping peaks in ATAC-seq data
A: decideTests() options in LIMMA
A: Removing cell cycle genes in large data set integration
A: Removing cell cycle genes in large data set integration
Answer: Quick two questions on limpa
Awards • All
Teacher to Gordon Smyth 53k
Popular Question to poojitha.stemcell ▴ 10
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.3k
Popular Question to helucro ▴ 70
Locations • All
The city by the bay, 17 minutes ago
United States, 28 minutes ago
United States, 34 minutes ago
United States, 57 minutes ago
United States, 1 hour ago
Traffic: 1235 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