Showing : limma • reset
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Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 3 days ago by 53k • written 3 days ago by • 0
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4
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206
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voomLmFit fitted log-CPM values
limma edgeR
updated 8 days ago by 53k • written 10 days ago by ▴ 10
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3
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214
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ROAST compare results with complex design
limma mroast roast CAMERA
written 12 days ago by • 0
2
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8
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447
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Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 12 days ago by 53k • written 4 weeks ago by ▴ 30
3
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3
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268
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p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 28 days ago by 53k • written 29 days ago by • 0
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1
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139
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Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
updated 4 weeks ago by 53k • written 4 weeks ago by ▴ 10
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2
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214
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Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
5 weeks ago richardallenfriedmanbrooklyn ▴ 30
3
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1
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233
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Limpa Pipeline Order
limma limpa
updated 5 weeks ago by 53k • written 5 weeks ago by • 0
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2
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284
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Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 5 weeks ago by 53k • written 5 weeks ago by ▴ 10
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8
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How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
5 weeks ago Jiahao Tian • 0
2
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2
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295
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Limma : paired samples leading to unexpected estimates
limma
6 weeks ago Basti ▴ 780
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2
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290
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(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
6 weeks ago sandmann.t ▴ 70
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8
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1.7k
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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
9 weeks ago • updated 8 weeks ago richardallenfriedmanbrooklyn ▴ 30
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9
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5.4k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
9 weeks ago • updated 8 weeks ago bbao ▴ 10
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1
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1.2k
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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 9 weeks ago by 53k • written 16.6 years ago by ▴ 10
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3
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2.2k
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Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma Bioconductor Metabolomics
updated 10 weeks ago by 53k • written 10 weeks ago by • 0
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4
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1.6k
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How to use goana function with zebrafish genome from org.Dr.eg.db
org.Dr.eg.db zebrafish limma
3 months ago • updated 12 weeks ago Eric • 0
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2
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6.2k
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limma duplicateCorrelation appropriate where some blocks cross condition and some are in same condition?
limma
3 months ago Geoff • 0
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3
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1.2k
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Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
3 months ago Paulito • 0
0
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1
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403
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Typo in the help of lmFit()
limma
updated 3 months ago by 53k • written 3 months ago by • 0
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2
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607
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Limma suqeezeVar
limma
3 months ago Mengchun • 0
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566
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Limma trend with limpa
limpa limma trend
updated 3 months ago by 53k • written 3 months ago by • 0
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5
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1.1k
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Dealing with heteroscedascity in limma
limma splines Proteomics
written 4 months ago by • 0
5
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7
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3.2k
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limma correction for tumor purity
limma
4 months ago gabriella.jacobson-eisenberg ▴ 20
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3
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Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 5 months ago by ▴ 10
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6
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2.9k
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Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
4 months ago • updated 3 months ago massimo • 0
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394
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Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
4 months ago jamiecatalano2 • 0
2
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1
reply
634
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ROAST for small sets
limma mroast
updated 4 months ago by 53k • written 4 months ago by • 0
2
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4
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1.7k
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how to use `arrayWeightsQuick()`?
limma
updated 4 months ago by • 0 • written 5 months ago by • 0
2
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2
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1.4k
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Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 5 months ago by ★ 4.9k • written 5 months ago by • 0
2
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4
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907
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Explanation for ROAST results
CAMERA limma
written 5 months ago by • 0
5
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3
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1.1k
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Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 5 months ago by 53k • written 6 months ago by ▴ 10
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2
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1.4k
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Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
6 months ago Elizabeth • 0
1
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2
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997
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Differential expression of proteins using somascan data
somascan limma
written 6 months ago by • 0
2
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4
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1.3k
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Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
6 months ago svlachavas ▴ 840
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5
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1.8k
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Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 8 months ago by 68k • written 8 months ago by ▴ 10
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0
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326
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
8 months ago GJ • 0
0
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2
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609
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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 8 months ago by ▴ 840
2
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5
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716
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Differential variability modelling with vst() expression
limma DESeq2
written 8 months ago by • 0
6
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5
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975
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 8 months ago by 68k • written 8 months ago by • 0
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724
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Cross-validation with multiple control subgroups in limma
limma multtest
8 months ago Ali Barry ▴ 40
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9
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1.4k
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 9 months ago by ▴ 30
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2
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616
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
9 months ago Tadeoye ▴ 20
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2
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819
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 9 months ago by 53k • written 9 months ago by ▴ 10
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3
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1.6k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 9 months ago by 68k • written 9 months ago by ▴ 10
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2
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656
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contrast matrix design for a continuous variable
limma
9 months ago • updated 7 months ago dtzhu337 • 0
3
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3
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950
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Crossover design with limma
limma crossover
updated 9 months ago by 53k • written 9 months ago by ▴ 30
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9
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1.5k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 9 months ago by 68k • written 9 months ago by • 0
6
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10
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3.2k
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What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 9 months ago by ★ 4.9k • written 9 months ago by ▴ 10
1
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3
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708
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Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 9 months ago by • 0
4,224 results • Page 1 of 85
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Comment: Heatmap of the Count Matrix by ArnulfoByrd • 0
Perhaps PCA loadings offer a more comprehensive perspective. Now, thinking back, I recall struggling with a similar data reduction dilemma …
Answer: readBam vs read_bam_insert_metrics by James W. MacDonald 68k
Depends on what you mean by input. If you mean to ask if you use `readBam` to generate something to use as an argument to `read_bam_insert_…
Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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