Showing : LIMMA • reset
1
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4
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1.5k
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limma design model for categorical variable
DNAMethylation limmaGUI biostatistics limma
updated 23 months ago by 53k • written 23 months ago by ▴ 10
4
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3
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1.2k
views
voom with quality weights after RUV correction
RUVSeq limma DifferentialExpression
updated 23 months ago by 53k • written 23 months ago by • 0
2
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3
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1.2k
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TMM normalization after RUVg correction
RUVSeq limma DifferentialExpression edgeR Normalization
updated 23 months ago by 68k • written 23 months ago by • 0
1
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2
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2.5k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 2.7 years ago by • 0
0
votes
2
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760
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Pairwise analysis of DESeq result and limma result
DESeq2 limma
23 months ago Lily Cheang ▴ 10
1
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2
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1.1k
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Longitudinal analysis in Limma
limma
24 months ago • updated 23 months ago COPD_Project • 0
2
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2
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1.3k
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Using limma for controlling age variable
linearmodeling limma
24 months ago Matej • 0
4
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6
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1.8k
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 23 months ago by 53k • written 2.0 years ago by • 0
0
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5
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2.1k
views
Can SVs identified from sva be used for removeBatchEffect() in DESeq2
sva DESeq2 BatchEffect limma
updated 2.0 years ago by ★ 5.0k • written 2.0 years ago by • 0
2
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4
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1.3k
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 2.0 years ago by 53k • written 2.1 years ago by • 0
1
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2
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863
views
Assess fit of variance prior
limma
updated 2.1 years ago by 53k • written 2.1 years ago by ▴ 30
2
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1
reply
657
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removeBatchEffect with non-linear model fit
limma DESeq2
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
2
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4
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1.9k
views
Correct the batch effect in methylation analysis in R
BatchEffect limma methylationArrayAnalysis
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
0
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3
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953
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Agilent Microarray Gene Oncology analysis gone wrong
AgilentChip limma goana
updated 2.1 years ago by ▴ 360 • written 2.1 years ago by • 0
5
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2
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1.7k
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
12
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5
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5.4k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 7 months ago by • 0 • written 2.1 years ago by • 0
0
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0
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738
views
multipollutant models
statistics Regression r limma
2.1 years ago Jitendra ▴ 10
0
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3
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1.4k
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
2.2 years ago • updated 2.1 years ago Karthik • 0
1
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1
reply
777
views
Limma/DESeq2 for unbalanced nested design (paired samples)
limma DESeq2
updated 2.1 years ago by 43k • written 2.2 years ago by • 0
3
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4
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1.5k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
2.2 years ago pl23 • 0
2
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4
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1.5k
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
2.2 years ago Tyler Sagendorf ▴ 10
1
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4
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1.6k
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controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
2.2 years ago Wending • 0
0
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4
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1.5k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 21 months ago by 43k • written 2.2 years ago by • 0
0
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5
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1.5k
views
Limma continuous design (association polygenic risk score with gene expression)
limma
updated 2.1 years ago by 53k • written 2.2 years ago by • 0
0
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5
replies
1.9k
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
2.3 years ago dorota.komar • 0
0
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1
reply
864
views
Issue with weights in voomLmFit()
limma
updated 14 months ago by 53k • written 2.3 years ago by ▴ 170
2
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1
reply
1.6k
views
limma::topTable with adjust.method=NULL is not BH corrected (manual is inconsistent with behavior?)
Bioconductor biocon limma
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
1
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7
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1.9k
views
DuplicateCorrelation() block by duplicate sample or by cell line ?
variancePartition RNASeqData limma BulkRNAseq RNASeq
updated 2.1 years ago by 53k • written 2.3 years ago by • 0
5
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3
replies
1.3k
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom blocking limma
updated 2.3 years ago by 53k • written 2.3 years ago by ▴ 180
5
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9
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2.9k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 21 months ago by 53k • written 2.3 years ago by ▴ 10
0
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1
reply
861
views
''Model_Matrix'' error
DifferentialExpression limma
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
1
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6
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3.8k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 9.2 years ago by ▴ 10
0
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0
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581
views
Huge effect of a single sample on DEGs
limma
2.3 years ago Jonathan ▴ 10
1
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1
reply
824
views
Further analysis after limma regression output
statistics Epigenetics limma
updated 2.3 years ago by 68k • written 2.3 years ago by ▴ 10
3
votes
3
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1.1k
views
comparing contrasts in edger/lima using makeContrasts function
DifferentialExpression edgeR limma
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
3
votes
3
replies
3.8k
views
Differential expression analysis with only FPKM matrix available from total newbie in R
FPKM RNASeqData DEAnalysis limma
2.3 years ago Ethan Nguyen • 0
1
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2
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2.1k
views
Should I use CPM or Voom transformed values for downstream analysis?
edgeR limma
2.3 years ago petertam1343 • 0
0
votes
6
replies
1.6k
views
Help with model.matrix and creating the right contrast matrix for limma
limma
2.4 years ago • updated 2.1 years ago rober204 • 0
6
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5
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13k
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Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 2.4 years ago by 53k • written 4.2 years ago by ▴ 340
4
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5
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1.6k
views
Phenotype effect - building a contrast matrix - grouping vs interaction
limma
updated 2.3 years ago by 53k • written 2.4 years ago by ▴ 10
3
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13
replies
2.4k
views
Timely differentially expressed genes
timecoursedata limma
2.4 years ago • updated 2.1 years ago triZZla • 0
0
votes
1
reply
873
views
Is it possible to combine count gene expression data coming from one sequencing technology (RNA seq) with intensity gene expression data coming from …
DESeq2 RNASeqData edgeR limma DifferentialExpression
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
1
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6
replies
1.7k
views
Limma dispersed distribution of log fold change
limma
written 2.4 years ago by • 0
1
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0
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914
views
Differential abundance analysis of phosphoproteomics data with multiple time points and conditions
Proteomics DifferentialRegulation limma
2.4 years ago svlachavas ▴ 840
0
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2
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923
views
How to incorporate covariate factors into design to analyse a continuous variable?
DifferentialMethylation limma
written 2.4 years ago by • 0
1
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3
replies
1.5k
views
Can CAMERA analyze just one particular pathway
pathway ORA limma CAMERA DGE
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
5
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5
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1.7k
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
2.4 years ago Jitendra ▴ 10
2
votes
5
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3.0k
views
removing the batch effect for vst counts and defining the batches in removeBatchEffect function
DESeq2 BatchEffect limma
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
2
votes
3
replies
3.2k
views
bulk RNA-seq analysis using R : batch effect : One question concerning Combat-seq and one question concerning DESeq2 design = batch + condition
BatchEffect sva DESeq2 RNASeqData limma
updated 2.4 years ago by 68k • written 2.4 years ago by ▴ 10
6
votes
7
replies
1.6k
views
Adding a group of samples reduces DEGs in other groups
RNASeq limma
updated 2.5 years ago by 53k • written 2.5 years ago by ▴ 10
4,230 results • Page 4 of 85
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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Martin Morgan 25k
I see rstudioapi in the `sessionInfo()`. RStudio does not support forked ('multicore') processes. Does the BiocParallel example work when y…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
Given that this is an issue with BiocParallel on your machine and we have a minimal reproducible example, you may want to repost the issue.…
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by ATpoint ★ 5.0k
Yes, still it's not reproducible, yet hard to debug. I cannot reproduce myself either.
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Benjamin • 0
Still happening using pre-existing size factors estimating dispersions gene-wise dispersion estimates: 15 workers mean-dis…
Answer: BiocParallel (and DESeq2) - wrong args for environment subassignment by Benjamin • 0
Still happening in a clean install
Votes
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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