Showing : Limma • reset
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two questions about limma
Microarray limma Microarray limma
updated 9 days ago by 53k • written 18.8 years ago by ▴ 240
2
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2
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252
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Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
20 days ago • updated 19 days ago jamie.gearing ▴ 60
1
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2
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342
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Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 3 months ago by ▴ 10
0
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1
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210
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 9 weeks ago by 53k • written 9 weeks ago by • 0
5
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13
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1.3k
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Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 10 weeks ago by 53k • written 12 weeks ago by • 0
0
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4
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424
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voomLmFit fitted log-CPM values
limma edgeR
updated 3 months ago by 53k • written 3 months ago by ▴ 10
1
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3
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364
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ROAST compare results with complex design
limma mroast roast CAMERA
written 3 months ago by • 0
2
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8
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730
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Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 3 months ago by 53k • written 3 months ago by ▴ 30
3
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4
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516
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p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 11 weeks ago by • 0 • written 3 months ago by • 0
1
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2
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373
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Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
4 months ago richardallenfriedmanbrooklyn ▴ 30
3
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1
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370
views
Limpa Pipeline Order
limma limpa
updated 4 months ago by 53k • written 4 months ago by • 0
3
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2
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449
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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
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8
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635
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How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
4 months ago Jiahao Tian • 0
2
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2
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418
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Limma : paired samples leading to unexpected estimates
limma
4 months ago Basti ▴ 780
2
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2
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515
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(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
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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
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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
5 months ago • updated 4 months ago bbao ▴ 10
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1
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1.4k
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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 16.8 years ago by ▴ 10
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3
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2.3k
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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
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4
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1.8k
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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
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6.4k
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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
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Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
6 months ago Paulito • 0
0
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1
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485
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Typo in the help of lmFit()
limma
updated 6 months ago by 53k • written 6 months ago by • 0
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2
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669
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Limma suqeezeVar
limma
6 months ago Mengchun • 0
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2
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1.3k
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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
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Dealing with heteroscedascity in limma
limma splines Proteomics
written 7 months ago by • 0
5
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7
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3.4k
views
limma correction for tumor purity
limma
7 months ago gabriella.jacobson-eisenberg ▴ 20
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3
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992
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Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 8 months ago by ▴ 10
4
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7
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3.3k
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Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
7 months ago • updated 8 weeks ago massimo ▴ 10
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0
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461
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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
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1
reply
702
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ROAST for small sets
limma mroast
updated 7 months ago by 53k • written 7 months ago by • 0
2
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4
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1.9k
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how to use `arrayWeightsQuick()`?
limma
updated 7 months ago by • 0 • written 8 months ago by • 0
2
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2
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1.5k
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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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985
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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
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1.6k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
9 months ago • updated 8 months ago Elizabeth • 0
1
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2
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1.1k
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Differential expression of proteins using somascan data
somascan limma
written 9 months ago by • 0
2
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4
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1.5k
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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
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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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382
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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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675
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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 11 months ago by ▴ 840
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5
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807
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Differential variability modelling with vst() expression
limma DESeq2
written 11 months ago by • 0
6
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5
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1.1k
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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
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2
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799
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Cross-validation with multiple control subgroups in limma
limma multtest
11 months ago Ali Barry ▴ 40
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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
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2
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716
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
12 months ago Tadeoye ▴ 20
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2
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931
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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
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3
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1.8k
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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
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2
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729
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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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1.1k
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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: 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…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
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 James W. MacDonald 68k
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
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