Showing : limma • reset
2
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5
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Dealing with heteroscedascity in limma
limma splines Proteomics
written 9 days ago by • 0
5
votes
7
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2.8k
views
limma correction for tumor purity
limma
9 days ago • updated 3 days ago gabriella.jacobson-eisenberg ▴ 20
0
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5
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648
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Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
18 days ago • updated 10 hours ago massimo • 0
0
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0
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241
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Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
19 days ago jamiecatalano2 • 0
2
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1
reply
449
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ROAST for small sets
limma mroast
updated 22 days ago by 52k • written 23 days ago by • 0
2
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4
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1.6k
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how to use `arrayWeightsQuick()`?
limma
updated 9 days ago by • 0 • written 5 weeks ago by • 0
0
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3
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679
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Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 5 weeks ago by ▴ 10
2
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2
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1.3k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 7 weeks ago by ★ 4.8k • written 7 weeks ago by • 0
2
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3
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726
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Explanation for ROAST results
CAMERA limma
updated 7 weeks ago by 52k • written 7 weeks ago by • 0
5
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3
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873
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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 weeks ago by 52k • written 8 weeks ago by ▴ 10
2
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2
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1.2k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
9 weeks ago • updated 8 weeks ago Elizabeth • 0
1
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2
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872
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Differential expression of proteins using somascan data
somascan limma
written 9 weeks ago by • 0
2
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4
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1.1k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
12 weeks ago • updated 10 weeks ago svlachavas ▴ 840
3
votes
5
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1.5k
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Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 3 months ago by 68k • written 3 months ago by ▴ 10
0
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0
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222
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
4 months ago GJ • 0
0
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2
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519
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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 4 months ago by ▴ 840
2
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5
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551
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Differential variability modelling with vst() expression
limma DESeq2
written 4 months ago by • 0
6
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5
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792
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 4 months ago by 68k • written 4 months ago by • 0
0
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2
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591
views
Cross-validation with multiple control subgroups in limma
limma multtest
4 months ago Ali Barry ▴ 40
1
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9
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1.1k
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 4 months ago by ▴ 30
0
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2
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454
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
5 months ago Tadeoye ▴ 20
0
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2
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644
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 5 months ago by 52k • written 5 months ago by ▴ 10
2
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3
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1.4k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 5 months ago by 68k • written 5 months ago by ▴ 10
1
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2
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550
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contrast matrix design for a continuous variable
limma
5 months ago • updated 3 months ago dtzhu337 • 0
0
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9
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1.3k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 5 months ago by 68k • written 5 months ago by • 0
3
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3
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820
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Crossover design with limma
limma crossover
updated 4 months ago by 52k • written 5 months ago by ▴ 30
6
votes
10
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3.0k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 5 months ago by ★ 4.8k • written 5 months ago by ▴ 10
1
vote
3
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589
views
Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 5 months ago by • 0
1
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2
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363
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Limma Interaction Effect with Covariates
limma DMRcate
5 months ago kitzhu • 0
4
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2
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827
views
Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 5 months ago by 52k • written 5 months ago by ▴ 60
0
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2
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302
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List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
5 months ago giulia.gentile ▴ 10
2
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3
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1.1k
views
[How to construct a model.matrix ]
limma modelmatrix
updated 5 months ago by 52k • written 6 months ago by • 0
3
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4
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914
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
6 months ago dseauer • 0
1
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3
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615
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
6 months ago • updated 5 months ago abadgerw • 0
0
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5
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908
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
6 months ago • updated 5 months ago abadgerw • 0
1
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2
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1.1k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
6 months ago Ai • 0
1
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8
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2.0k
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Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 6 months ago by • 0
3
votes
3
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1.2k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 6 months ago by • 0
2
votes
12
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2.2k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
6 months ago • updated 5 months ago john • 0
4
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3
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993
views
Analysis of 2*4 factorial design
limma
updated 6 months ago by 52k • written 6 months ago by • 0
4
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6
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1.7k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 6 months ago by 52k • written 6 months ago by • 0
4
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6
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1.5k
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Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
6 months ago altintas.ali • 0
2
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2
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622
views
Automatically generate contrasts from a model matrix / formula
limma
updated 7 months ago by ★ 4.8k • written 7 months ago by ▴ 10
0
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3
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601
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Need help interpreting heatmaps from limma
limma
written 7 months ago by • 0
3
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3
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500
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
7 months ago Guido Hooiveld ★ 4.1k
2
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1
reply
1.8k
views
Removing Effect of Covariate in Only a Subset of Samples in a Model Containing All Samples Loses Full Rank if Factor but not Numerical
limma
updated 7 months ago by 68k • written 7 months ago by ▴ 10
5
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4
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763
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 7 months ago by ★ 4.8k • written 7 months ago by • 0
0
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0
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355
views
Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
7 months ago tim.meese • 0
0
votes
2
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586
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 7 months ago by 52k • written 7 months ago by • 0
1
vote
2
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667
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 7 months ago by 43k • written 7 months ago by ▴ 10
50 results • Page 1 of 1
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Comment: limma::voom vs edgeR::voomLmFit - when to use? by Geoff • 0
Just wondering--why was this function put into `edgeR` rather than `limma`? Maybe a bit technical, but it is a little confusing from an out…
Comment: cannot download atena annotation for human by Davide • 0
Hi Robert, I was able to solve the problem. Indeed, it stems from the co-occurrence of two different AnnotationHub available for hg38. …
Comment: Setting ylims in bam coverage plot and assigning compound sashimi numbers to ove by macdonaldfrench7286566 • 0
Regarding the ylim for the coverage [space waves][1], have you tried accessing the ylim slot of the CoverageTrack object after you've creat…
Comment: How to left_join a tidySummarizedExperiment with a GRanges object by seqnames an by Kateřina • 0
I unfortunately haven't. Non-tidy grammar is fine, but I have wanted to use tidy-only grammar. Thank you nonetheless!
Comment: GAlignments Cigar to GRanges by pineiroalejandro • 0
Wow, so easy! Thanks for your quick reply.
Votes
Answer: GAlignments Cigar to GRanges
Answer: GAlignments Cigar to GRanges
When running contrasts, does it use normalized read counts?
When running contrasts, does it use normalized read counts?
Importing Salmon counts with tximport with host and virus genomes
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