Showing : limma • reset
2
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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
1 day ago • updated 5 hours ago richardallenfriedmanbrooklyn ▴ 30
2
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5
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1.7k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
updated 13 hours ago by • 0 • written 3 days ago by ▴ 10
0
votes
1
reply
1.1k
views
How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray limma BRAIN Microarray limma BRAIN
updated 3 days ago by 52k • written 16.4 years ago by ▴ 10
0
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3
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2.0k
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Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma Bioconductor Metabolomics
updated 9 days ago by 52k • written 13 days ago by • 0
0
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4
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1.5k
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How to use goana function with zebrafish genome from org.Dr.eg.db
org.Dr.eg.db zebrafish limma
28 days ago • updated 27 days ago Eric • 0
3
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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
6 weeks ago Geoff • 0
2
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3
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1.2k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
7 weeks ago Paulito • 0
0
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1
reply
330
views
Typo in the help of lmFit()
limma
updated 7 weeks ago by 52k • written 7 weeks ago by • 0
0
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2
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548
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Limma suqeezeVar
limma
8 weeks ago • updated 7 weeks ago Mengchun • 0
0
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2
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483
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Limma trend with limpa
limpa limma trend
updated 6 weeks ago by 52k • written 8 weeks 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 9 weeks ago by • 0
5
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7
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3.1k
views
limma correction for tumor purity
limma
9 weeks ago gabriella.jacobson-eisenberg ▴ 20
0
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3
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806
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Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 3 months ago by ▴ 10
2
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6
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2.7k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
11 weeks ago • updated 7 weeks ago massimo • 0
0
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0
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337
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Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
11 weeks ago jamiecatalano2 • 0
2
votes
1
reply
589
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ROAST for small sets
limma mroast
updated 11 weeks ago by 52k • written 11 weeks ago by • 0
2
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4
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1.7k
views
how to use `arrayWeightsQuick()`?
limma
updated 9 weeks ago by • 0 • written 3 months ago by • 0
2
votes
2
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1.3k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 3 months ago by ★ 4.9k • written 3 months ago by • 0
2
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3
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807
views
Explanation for ROAST results
CAMERA limma
updated 3 months ago by 52k • written 3 months ago by • 0
5
votes
3
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988
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Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 3 months ago by 52k • written 3 months ago by ▴ 10
2
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2
replies
1.3k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
4 months ago • updated 3 months ago Elizabeth • 0
1
vote
2
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951
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Differential expression of proteins using somascan data
somascan limma
written 4 months ago by • 0
2
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4
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1.2k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
4 months ago svlachavas ▴ 840
3
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5
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1.7k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 5 months ago by 68k • written 5 months ago by ▴ 10
0
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0
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276
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
6 months ago GJ • 0
0
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2
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567
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 6 months ago by ▴ 840
2
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5
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640
views
Differential variability modelling with vst() expression
limma DESeq2
written 6 months ago by • 0
6
votes
5
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903
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 6 months ago by 68k • written 6 months ago by • 0
0
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2
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660
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Cross-validation with multiple control subgroups in limma
limma multtest
6 months ago Ali Barry ▴ 40
1
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9
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1.2k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 6 months ago by ▴ 30
0
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2
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539
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
7 months ago Tadeoye ▴ 20
0
votes
2
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734
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 7 months ago by 52k • written 7 months ago by ▴ 10
2
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3
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1.5k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 7 months ago by 68k • written 7 months ago by ▴ 10
1
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2
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613
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contrast matrix design for a continuous variable
limma
7 months ago • updated 5 months ago dtzhu337 • 0
3
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3
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894
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Crossover design with limma
limma crossover
updated 6 months ago by 52k • written 7 months ago by ▴ 30
0
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9
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1.4k
views
Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 7 months ago by 68k • written 7 months ago by • 0
6
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10
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3.1k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 7 months ago by ★ 4.9k • written 7 months ago by ▴ 10
1
vote
3
replies
654
views
Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 7 months ago by • 0
0
votes
2
replies
352
views
List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
7 months ago giulia.gentile ▴ 10
4
votes
2
replies
1.1k
views
Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 7 months ago by 52k • written 7 months ago by ▴ 60
1
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2
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430
views
Limma Interaction Effect with Covariates
limma DMRcate
7 months ago kitzhu • 0
2
votes
3
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1.2k
views
[How to construct a model.matrix ]
limma modelmatrix
updated 7 months ago by 52k • written 8 months ago by • 0
3
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4
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1.0k
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
8 months ago dseauer • 0
1
vote
3
replies
704
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
8 months ago • updated 7 months ago abadgerw • 0
0
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5
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1.0k
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
8 months ago • updated 7 months ago abadgerw • 0
1
vote
8
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2.2k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 8 months ago by • 0
1
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2
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1.2k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
8 months ago Ai • 0
3
votes
3
replies
1.4k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 8 months ago by • 0
4
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3
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1.1k
views
Analysis of 2*4 factorial design
limma
updated 8 months ago by 52k • written 8 months ago by • 0
2
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12
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2.4k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
8 months ago • updated 7 months ago john • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Should Xenium pseudobulk experiments be analysed like microarrays (limma) or lik by richardallenfriedmanbrooklyn ▴ 30
He is of the opinion that the negative binomial model is appropriate to RNASeq because of sequencing and that since Xenium uses probes it i…
Comment: Should Xenium pseudobulk experiments be analysed like microarrays (limma) or lik by ATpoint ★ 4.9k
Would you share the rationale of your colleague for the sake of discussion?
Comment: Should Xenium pseudobulk experiments be analysed like microarrays (limma) or lik by richardallenfriedmanbrooklyn ▴ 30
Dear ATpoint, Thank you. That is also my understanding. A colleague thinks otherwise and specifically asked me to ask Gordon Smyth. I am a…
Comment: Should Xenium pseudobulk experiments be analysed like microarrays (limma) or lik by ATpoint ★ 4.9k
It's digital counts, not intensities, so naturally you would go with the RNA-seq methods.
Comment: HMP_2019_t2d data origin by Blan • 0
Thanks! However, I don't see anything regarding this study in particular. I would like to access the raw data. In the source publication ci…
Votes
Comment: Should Xenium pseudobulk experiments be analysed like microarrays (limma) or lik
Comment: Should Xenium pseudobulk experiments be analysed like microarrays (limma) or lik
Answer: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in
Comment: competitive enrichment test yields too few significant results, self-contained t
Answer: competitive enrichment test yields too few significant results, self-contained t
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