Showing : LIMMA • reset
2
votes
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
vote
2
replies
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
replies
746
views
Pairwise analysis of DESeq result and limma result
DESeq2 limma
23 months ago Lily Cheang ▴ 10
1
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2
replies
1.0k
views
Longitudinal analysis in Limma
limma
23 months ago COPD_Project • 0
2
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2
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1.2k
views
Using limma for controlling age variable
linearmodeling limma
23 months ago Matej • 0
4
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6
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1.7k
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 23 months ago by 53k • written 24 months ago by • 0
0
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5
replies
2.0k
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
votes
4
replies
1.2k
views
Different genes expression with limma
DESeq2 DifferentialExpression limma
updated 24 months ago by 53k • written 2.0 years ago by • 0
1
vote
2
replies
856
views
Assess fit of variance prior
limma
updated 2.1 years ago by 53k • written 2.1 years ago by ▴ 30
2
votes
1
reply
651
views
removeBatchEffect with non-linear model fit
limma DESeq2
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
2
votes
4
replies
1.8k
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
votes
3
replies
937
views
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
votes
2
replies
1.6k
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
votes
5
replies
5.2k
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
replies
730
views
multipollutant models
statistics Regression r limma
2.1 years ago Jitendra ▴ 10
0
votes
3
replies
1.3k
views
'Subtracting' counts on basis of Negative control media and water samples
limma edgeR RNASeq DESeq2
2.1 years ago Karthik • 0
1
vote
1
reply
765
views
Limma/DESeq2 for unbalanced nested design (paired samples)
limma DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
3
votes
4
replies
1.5k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
2.1 years ago pl23 • 0
2
votes
4
replies
1.5k
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
2.1 years ago Tyler Sagendorf ▴ 10
1
vote
4
replies
1.5k
views
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
votes
4
replies
1.4k
views
How to correct for known and surrogate variables in DESeq2?
DESeq2 BatchEffect sva limma
updated 20 months ago by 43k • written 2.2 years ago by • 0
0
votes
5
replies
1.4k
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
votes
5
replies
1.9k
views
minfi, limma, adjusting for cell counts - integrating the resoults of estimateCellCounts into the linear regression model
minfi limma
2.2 years ago dorota.komar • 0
0
votes
1
reply
857
views
Issue with weights in voomLmFit()
limma
updated 14 months ago by 53k • written 2.2 years ago by ▴ 170
2
votes
1
reply
1.5k
views
limma::topTable with adjust.method=NULL is not BH corrected (manual is inconsistent with behavior?)
Bioconductor biocon limma
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
1
vote
7
replies
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 2.2 years ago by • 0
5
votes
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 2.2 years ago by 53k • written 2.2 years ago by ▴ 180
5
votes
9
replies
2.9k
views
Batch correction and repeated measures
RUVSeq sva limma
updated 20 months ago by 53k • written 2.3 years ago by ▴ 10
0
votes
1
reply
853
views
''Model_Matrix'' error
DifferentialExpression limma
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
1
vote
6
replies
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 9.1 years ago by ▴ 10
0
votes
0
replies
578
views
Huge effect of a single sample on DEGs
limma
2.3 years ago Jonathan ▴ 10
1
vote
1
reply
809
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
replies
1.0k
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
3.6k
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
vote
2
replies
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
2.3 years ago • updated 2.1 years ago rober204 • 0
6
votes
5
replies
13k
views
Using Limma R package For Proteomics differential expression
limma ProteomicsWorkflow
updated 2.3 years ago by 53k • written 4.2 years ago by ▴ 340
4
votes
5
replies
1.6k
views
Phenotype effect - building a contrast matrix - grouping vs interaction
limma
updated 2.3 years ago by 53k • written 2.3 years ago by ▴ 10
3
votes
13
replies
2.4k
views
Timely differentially expressed genes
timecoursedata limma
2.3 years ago • updated 2.1 years ago triZZla • 0
0
votes
1
reply
866
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 2.3 years ago by ★ 5.0k • written 2.4 years ago by • 0
1
vote
6
replies
1.7k
views
Limma dispersed distribution of log fold change
limma
written 2.4 years ago by • 0
1
vote
0
replies
898
views
Differential abundance analysis of phosphoproteomics data with multiple time points and conditions
Proteomics DifferentialRegulation limma
2.4 years ago svlachavas ▴ 840
0
votes
2
replies
912
views
How to incorporate covariate factors into design to analyse a continuous variable?
DifferentialMethylation limma
written 2.4 years ago by • 0
1
vote
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
votes
5
replies
1.6k
views
limma output for epic array methylation data
linearregression epicarray MethylationArray limma
2.4 years ago Jitendra ▴ 10
2
votes
5
replies
2.9k
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
3.1k
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 2.4 years ago by 53k • written 2.4 years ago by ▴ 10
1
vote
2
replies
1.6k
views
loading scores using plotMDS in limma
plotMDS limma
2.4 years ago Cen • 0
2
votes
1
reply
1.2k
views
Grouping DEGs yields varying results
RNASeq limma
updated 2.4 years ago by 53k • written 2.4 years ago by ▴ 10
4,228 results • Page 4 of 85
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Comment: Converting Probe IDs to HGNC symbols by Manav ▴ 10
ah thank u so much
Comment: Guitar R package requires update due to dependency GenomicFeatures by Sean Davis 21k
A great way to communicate such a nice troubleshooting and bug fix hint is to file an issue in github: https://github.com/lzcyzm/Guitar/iss…
Answer: Converting Probe IDs to HGNC symbols by Sean Davis 21k
The brainarray annotations are very confusing, as the IDs in the fData look like affymetrix probe IDs. To clarify, the brainarray project m…
Comment: How to do differential expresion across time serise with edgeR? by Gordon Smyth 53k
If you have fake replicates, then I think my code answers your question about how to run the edgeR time-course analysis. Regarding tutoria…
Comment: How to do differential expresion across time serise with edgeR? by petergrahamclark ▴ 10
The use case is kinetic model parameterisation. I'm actually a systems biologist not a bioinformatician. (which is why I'm struggling here)…
Votes
Answer: Converting Probe IDs to HGNC symbols
Converting Probe IDs to HGNC symbols
Answer: How to install packages such as TCGAbiolinks, SumarizedExperiment?
A: limma-voom duplicateCorrelation once or twice, difference?
A: limma: comparison of repeat measurements - blocking or within-subject correlatio
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