Showing : Limma • reset
1
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ROAST compare results with complex design
limma mroast roast CAMERA
updated 3 hours ago by 52k • written 10 hours ago by • 0
2
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8
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381
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Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 3 hours ago by 52k • written 18 days ago by ▴ 30
3
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3
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223
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p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 16 days ago by 52k • written 17 days ago by • 0
1
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1
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118
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Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
updated 21 days ago by 52k • written 21 days ago by ▴ 10
1
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2
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190
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Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
25 days ago • updated 23 days ago richardallenfriedmanbrooklyn ▴ 30
2
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1
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191
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Limpa Pipeline Order
limma limpa
updated 27 days ago by 52k • written 28 days ago by • 0
2
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2
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248
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Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 27 days ago by 52k • written 29 days ago by ▴ 10
0
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8
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443
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How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
29 days ago • updated 25 days ago Jiahao Tian • 0
2
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2
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254
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Limma : paired samples leading to unexpected estimates
limma
4 weeks ago Basti ▴ 780
2
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2
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270
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(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
5 weeks ago • updated 4 weeks ago sandmann.t ▴ 70
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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
7 weeks ago richardallenfriedmanbrooklyn ▴ 30
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9
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5.3k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
7 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 7 weeks ago by 52k • 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 8 weeks ago by 52k • written 9 weeks ago by • 0
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
11 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
2
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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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393
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Typo in the help of lmFit()
limma
updated 3 months ago by 52k • written 3 months ago by • 0
0
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2
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599
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Limma suqeezeVar
limma
3 months ago Mengchun • 0
0
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2
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549
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Limma trend with limpa
limpa limma trend
updated 3 months ago by 52k • written 3 months ago by • 0
2
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5
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1.1k
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Dealing with heteroscedascity in limma
limma splines Proteomics
written 3 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
3 months ago gabriella.jacobson-eisenberg ▴ 20
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3
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872
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Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 4 months ago by ▴ 10
2
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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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0
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384
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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
626
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ROAST for small sets
limma mroast
updated 4 months ago by 52k • 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 3 months ago by • 0 • written 4 months ago by • 0
2
votes
2
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1.4k
views
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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3
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869
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Explanation for ROAST results
CAMERA limma
updated 5 months ago by 52k • 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 52k • written 5 months ago by ▴ 10
2
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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
5 months ago Elizabeth • 0
1
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2
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989
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Differential expression of proteins using somascan data
somascan limma
written 5 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 7 months ago by 68k • written 7 months ago by ▴ 10
0
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0
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317
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
7 months ago GJ • 0
0
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2
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600
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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 7 months ago by ▴ 840
2
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5
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691
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Differential variability modelling with vst() expression
limma DESeq2
written 7 months ago by • 0
6
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5
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953
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 7 months ago by 68k • written 8 months ago by • 0
0
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2
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713
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Cross-validation with multiple control subgroups in limma
limma multtest
8 months ago Ali Barry ▴ 40
1
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9
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1.3k
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 8 months ago by ▴ 30
0
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2
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592
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
8 months ago Tadeoye ▴ 20
0
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2
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794
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 8 months ago by 52k • written 9 months ago by ▴ 10
2
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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
1
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2
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645
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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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942
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Crossover design with limma
limma crossover
updated 8 months ago by 52k • written 9 months ago by ▴ 30
0
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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
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 8 months ago by ★ 4.9k • written 9 months ago by ▴ 10
1
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3
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697
views
Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 9 months ago by • 0
0
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2
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374
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List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
9 months ago giulia.gentile ▴ 10
4
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2
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1.1k
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Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 9 months ago by 52k • written 9 months ago by ▴ 60
4,222 results • Page 1 of 85
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Comment: ROAST compare results with complex design by Gordon Smyth 52k
It's also worth pointing out that the syntax for `camera` and `mroast` is the same, so I wonder how OP did the earlier `camera` analysis.
Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Votes
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
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