Showing : Limma • reset
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Cross-validation with multiple control subgroups in limma
limma multtest
updated 7 hours ago by 52k • written 19 hours ago by ▴ 40
1
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8
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577
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Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
updated 2 days ago by 52k • written 3 days ago by ▴ 30
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2
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255
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
11 days ago • updated 10 days ago Tadeoye ▴ 20
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2
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426
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sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 14 days ago by 52k • written 15 days ago by ▴ 10
2
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3
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1.1k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 16 days ago by 67k • written 16 days ago by ▴ 10
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2
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290
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contrast matrix design for a continuous variable
limma
18 days ago dtzhu337 • 0
3
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3
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562
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Crossover design with limma
limma crossover
updated 4 days ago by 52k • written 23 days ago by ▴ 30
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9
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789
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 16 days ago by 67k • written 21 days ago by • 0
6
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10
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2.4k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 12 days ago by ★ 4.6k • written 23 days ago by ▴ 10
1
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3
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393
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Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 28 days ago by • 0
0
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2
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176
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List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
4 weeks ago giulia.gentile ▴ 10
4
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2
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526
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Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 4 weeks ago by 52k • written 4 weeks ago by ▴ 50
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2
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170
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Limma Interaction Effect with Covariates
limma DMRcate
4 weeks ago kitzhu • 0
2
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3
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875
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[How to construct a model.matrix ]
limma modelmatrix
updated 4 weeks ago by 52k • written 5 weeks ago by • 0
3
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4
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622
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Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
5 weeks ago dseauer • 0
1
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3
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424
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makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
6 weeks ago • updated 23 days ago abadgerw • 0
0
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5
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617
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Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
6 weeks ago • updated 19 days ago abadgerw • 0
1
vote
8
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1.1k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 6 weeks ago by • 0
1
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2
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932
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Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
6 weeks ago Ai • 0
3
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3
replies
890
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 7 weeks ago by • 0
4
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3
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799
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Analysis of 2*4 factorial design
limma
updated 7 weeks ago by 52k • written 8 weeks ago by • 0
2
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12
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1.6k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
8 weeks ago • updated 29 days ago john • 0
4
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6
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1.5k
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LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 8 weeks ago by 52k • written 8 weeks ago by • 0
4
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6
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1.1k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
9 weeks ago • updated 7 weeks ago altintas.ali • 0
2
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2
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332
views
Automatically generate contrasts from a model matrix / formula
limma
updated 9 weeks ago by ★ 4.6k • written 9 weeks ago by ▴ 10
3
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3
replies
309
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
10 weeks ago • updated 9 weeks ago Guido Hooiveld ★ 4.1k
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3
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354
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Need help interpreting heatmaps from limma
limma
written 10 weeks ago by • 0
2
votes
1
reply
1.4k
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 10 weeks ago by 67k • written 10 weeks ago by ▴ 10
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4
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468
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 10 weeks ago by ★ 4.6k • written 11 weeks ago by • 0
1
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2
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473
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 12 weeks ago by 43k • written 12 weeks ago by ▴ 10
0
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0
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233
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Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
12 weeks ago tim.meese • 0
0
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2
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373
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EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 11 weeks ago by 52k • written 12 weeks ago by • 0
0
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2
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463
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Question on performing ANOVA-like analysis using limma
limma
updated 3 months ago by 52k • written 3 months ago by • 0
17
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9
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7.1k
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How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 3 months ago by 67k • written 8.6 years ago by ▴ 10
2
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1
reply
359
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 3 months ago by 67k • written 3 months ago by ▴ 10
0
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1
reply
615
views
Unable to install/use limma
limma Bioconductor
updated 3 months ago by 67k • written 3 months ago by • 0
3
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3
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531
views
voom does not seem to properly correct for library size
limma
updated 3 months ago by 52k • written 3 months ago by ★ 4.6k
1
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5
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840
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RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 3 months ago by 52k • written 4 months ago by • 0
0
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3
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554
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Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 4 months ago by 52k • written 4 months ago by • 0
3
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4
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612
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using limma trend workflow in CAMERA
CAMERA limma
4 months ago • updated 3 months ago Jay • 0
3
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3
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568
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One-sided tests with CAMERA-PR
CAMERA limma
updated 4 months ago by 52k • written 4 months ago by ▴ 10
1
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6
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711
views
limma and Syntactically Invalid Factor Values
limma
updated 4 months ago by 52k • written 5 months ago by ★ 1.5k
1
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1
reply
582
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma DSP GeomxTools
5 months ago Bioinformagician • 0
4
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3
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588
views
Limma comparing gene expression between base line and one treatment
limma
updated 5 months ago by 67k • written 5 months ago by • 0
0
votes
1
reply
544
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 5 months ago by ★ 4.6k • written 5 months ago by • 0
2
votes
5
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641
views
Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 5 months ago by 67k • written 5 months ago by • 0
4
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14
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1.7k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign limma pairedsamples
updated 4 months ago by 52k • written 5 months ago by • 0
3
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4
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831
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Differences in Limma and Dreamlet random effects from confounded dataset
limma dreamlet
5 months ago jcollier • 0
4
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4
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1.2k
views
Using both voom and removeBatchEffect, will they double adjust the data or is it the right way to perform this
limma adjustment voom removeBatchEffect covariates
6 months ago • updated 5 months ago sukeshinik5 ▴ 20
0
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1
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336
views
Deseq2 design matrix
DESeq2 Designmatrix limma
updated 5 months ago by 67k • written 6 months ago by • 0
50 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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