Showing : limma • reset
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two questions about limma
Microarray limma Microarray limma
updated 16 days ago by 53k • written 18.8 years ago by ▴ 240
2
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2
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264
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Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
27 days ago • updated 26 days ago jamie.gearing ▴ 60
1
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2
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353
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Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 4 months ago by ▴ 10
0
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1
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219
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 10 weeks ago by 53k • written 10 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 11 weeks ago by 53k • written 3 months ago by • 0
0
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4
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437
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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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375
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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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748
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Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 3 months ago by 53k • written 4 months ago by ▴ 30
3
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4
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537
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p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 3 months ago by • 0 • written 4 months ago by • 0
1
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2
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388
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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
reply
386
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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456
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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
0
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8
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652
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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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427
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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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524
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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
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
5 months ago richardallenfriedmanbrooklyn ▴ 30
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9
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5.7k
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competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
5 months ago bbao ▴ 10
0
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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 16.9 years ago by ▴ 10
0
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3
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2.4k
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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
6 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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489
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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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675
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Limma suqeezeVar
limma
7 months ago • updated 6 months ago Mengchun • 0
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 7 months ago by • 0
2
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5
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1.3k
views
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
0
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3
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1.0k
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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
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
7 months ago • updated 9 weeks ago massimo ▴ 10
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0
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470
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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
710
views
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
views
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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999
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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 9 months ago by 53k • written 9 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 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
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 11 months ago by 68k • written 11 months ago by ▴ 10
0
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0
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388
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
11 months ago GJ • 0
0
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2
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684
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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
2
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5
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825
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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
views
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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806
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Cross-validation with multiple control subgroups in limma
limma multtest
12 months ago • updated 11 months ago Ali Barry ▴ 40
1
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9
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1.6k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 12 months ago by ▴ 40
0
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2
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725
views
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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940
views
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
views
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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735
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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1.1k
views
Crossover design with limma
limma crossover
updated 12 months ago by 53k • written 12 months ago by ▴ 30
4,226 results • Page 1 of 85
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
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…
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
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