Showing : LIMMA • reset
2
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2
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228
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Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
11 days ago • updated 10 days ago jamie.gearing ▴ 60
1
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2
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332
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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
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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
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418
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voomLmFit fitted log-CPM values
limma edgeR
updated 12 weeks ago by 53k • written 12 weeks ago by ▴ 10
1
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3
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357
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ROAST compare results with complex design
limma mroast roast CAMERA
written 12 weeks ago by • 0
2
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8
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717
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Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 12 weeks ago by 53k • written 3 months ago by ▴ 30
3
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4
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502
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p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 10 weeks ago by • 0 • written 3 months ago by • 0
1
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2
replies
356
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
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2
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435
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
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8
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620
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How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
3 months ago Jiahao Tian • 0
2
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2
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409
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Limma : paired samples leading to unexpected estimates
limma
4 months ago Basti ▴ 780
2
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2
replies
503
views
(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
4 months ago sandmann.t ▴ 70
4
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8
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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
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9
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5.6k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
4 months ago bbao ▴ 10
0
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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
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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
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3
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1.5k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
6 months ago Paulito • 0
0
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1
reply
475
views
Typo in the help of lmFit()
limma
updated 6 months ago by 53k • written 6 months ago by • 0
0
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2
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659
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Limma suqeezeVar
limma
6 months ago Mengchun • 0
0
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2
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1.3k
views
Limma trend with limpa
limpa limma trend
updated 6 months ago by 53k • written 6 months ago by • 0
2
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5
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1.2k
views
Dealing with heteroscedascity in limma
limma splines Proteomics
written 6 months ago by • 0
5
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7
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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
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0
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451
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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
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4
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974
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Explanation for ROAST results
CAMERA limma
written 8 months ago by • 0
5
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3
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1.2k
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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
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2
replies
1.6k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
8 months ago Elizabeth • 0
1
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2
replies
1.1k
views
Differential expression of proteins using somascan data
somascan limma
written 8 months ago by • 0
2
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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
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5
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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
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0
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380
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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
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2
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668
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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
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5
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796
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Differential variability modelling with vst() expression
limma DESeq2
written 10 months ago by • 0
6
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5
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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
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2
replies
793
views
Cross-validation with multiple control subgroups in limma
limma multtest
11 months ago Ali Barry ▴ 40
1
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9
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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
709
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
11 months ago Tadeoye ▴ 20
0
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2
replies
915
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
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3
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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
721
views
contrast matrix design for a continuous variable
limma
12 months ago • updated 10 months ago dtzhu337 • 0
3
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3
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1.0k
views
Crossover design with limma
limma crossover
updated 11 months ago by 53k • written 12 months ago by ▴ 30
0
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9
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1.8k
views
Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 11 months ago by 68k • written 12 months ago by • 0
4,226 results • Page 1 of 85
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Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
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.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
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
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