Showing : Limma • reset
5
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Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 2 days ago by 52k • written 2 days ago by ▴ 10
0
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0
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32
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Limma: twin study with mono & dizygotic, discordant and concordant pairs
twins limma formula design
7 days ago Geoff • 0
2
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2
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1.1k
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Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
10 days ago • updated 4 days ago Elizabeth • 0
1
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2
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727
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Differential expression of proteins using somascan data
somascan limma
written 14 days ago by • 0
2
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4
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877
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Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
4 weeks ago • updated 17 days ago svlachavas ▴ 840
3
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5
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1.2k
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Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 9 weeks ago by 68k • written 9 weeks ago by ▴ 10
0
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0
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176
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
9 weeks ago GJ • 0
0
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2
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447
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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 10 weeks ago by ▴ 840
2
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5
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429
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Differential variability modelling with vst() expression
limma DESeq2
written 10 weeks ago by • 0
6
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5
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677
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How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 10 weeks ago by 68k • written 11 weeks ago by • 0
0
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2
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537
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Cross-validation with multiple control subgroups in limma
limma multtest
3 months ago • updated 12 weeks ago Ali Barry ▴ 40
1
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9
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970
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 3 months ago by ▴ 30
0
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2
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395
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
3 months ago Tadeoye ▴ 20
0
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2
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570
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 3 months ago by 52k • written 3 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 3 months ago by 68k • written 3 months ago by ▴ 10
1
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2
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494
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contrast matrix design for a continuous variable
limma
3 months ago • updated 8 weeks ago dtzhu337 • 0
3
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3
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734
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Crossover design with limma
limma crossover
updated 3 months ago by 52k • written 3 months ago by ▴ 30
0
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9
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1.1k
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 3 months ago by 68k • written 3 months ago by • 0
6
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10
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2.8k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 3 months ago by ★ 4.7k • written 3 months ago by ▴ 10
1
vote
3
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529
views
Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 3 months ago by • 0
0
votes
2
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271
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List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
4 months ago giulia.gentile ▴ 10
4
votes
2
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691
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Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 4 months ago by 52k • written 4 months ago by ▴ 50
1
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2
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312
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Limma Interaction Effect with Covariates
limma DMRcate
4 months ago kitzhu • 0
2
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3
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1.0k
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[How to construct a model.matrix ]
limma modelmatrix
updated 4 months ago by 52k • written 4 months ago by • 0
3
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4
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815
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
4 months ago dseauer • 0
1
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3
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552
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
4 months ago • updated 3 months ago abadgerw • 0
0
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5
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808
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
4 months ago • updated 3 months ago abadgerw • 0
1
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8
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1.7k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 4 months ago by • 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
4 months ago Ai • 0
3
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3
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1.1k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 4 months ago by • 0
4
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3
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916
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Analysis of 2*4 factorial design
limma
updated 4 months ago by 52k • written 4 months ago by • 0
2
votes
12
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2.0k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
4 months ago • updated 3 months ago john • 0
4
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6
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1.7k
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LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 4 months ago by 52k • written 5 months ago by • 0
4
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6
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1.4k
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Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
5 months ago • updated 4 months ago altintas.ali • 0
2
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2
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516
views
Automatically generate contrasts from a model matrix / formula
limma
updated 5 months ago by ★ 4.7k • written 5 months ago by ▴ 10
3
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3
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433
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
5 months ago Guido Hooiveld ★ 4.1k
0
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3
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523
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Need help interpreting heatmaps from limma
limma
written 5 months ago by • 0
2
votes
1
reply
1.7k
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 5 months ago by 68k • written 5 months ago by ▴ 10
5
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4
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664
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 5 months ago by ★ 4.7k • written 5 months ago by • 0
1
vote
2
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605
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 5 months ago by 43k • written 5 months ago by ▴ 10
0
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0
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302
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
5 months ago tim.meese • 0
0
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2
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510
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 5 months ago by 52k • written 5 months ago by • 0
0
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2
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576
views
Question on performing ANOVA-like analysis using limma
limma
updated 6 months ago by 52k • written 6 months ago by • 0
17
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9
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7.4k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 6 months ago by 68k • written 8.8 years ago by ▴ 10
2
votes
1
reply
473
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 6 months ago by 68k • written 6 months ago by ▴ 10
0
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1
reply
1.3k
views
Unable to install/use limma
limma Bioconductor
updated 6 months ago by 68k • written 6 months ago by • 0
3
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3
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701
views
voom does not seem to properly correct for library size
limma
updated 6 months ago by 52k • written 6 months ago by ★ 4.7k
1
vote
5
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1.0k
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 6 months ago by 52k • written 7 months ago by • 0
0
votes
3
replies
667
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 7 months ago by 52k • written 7 months ago by • 0
3
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4
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802
views
using limma trend workflow in CAMERA
CAMERA limma
7 months ago • updated 6 months ago Jay • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
A: use tximport's countsFromAbundance when using DESeq2
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