Showing : LIMMA • reset
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1.1k
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specifying comparison of interest in the minfi Bumhunter function
limma bumphunter methylationArrayAnalysis minfi
updated 2.9 years ago by 68k • written 2.9 years ago by • 0
2
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2
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1.4k
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Question about avereps function of limma
avereps probes average limma Microarray
updated 2.9 years ago by 53k • written 2.9 years ago by ▴ 10
0
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2
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1.2k
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Is there any reason to think that normalization (e.g. TMM) doesn't work well with samples that that have very different raw counts?
limma RNASeqData edgeR
updated 2.9 years ago by ▴ 40 • written 2.9 years ago by • 0
0
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1
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958
views
Microarray Data - Matching Probe ID's to Gene Expression Symbols
limma
updated 2.9 years ago by ★ 4.0k • written 2.9 years ago by • 0
1
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3
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1.3k
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Calculating the contrast of two genotypes "vs"
limma
updated 2.9 years ago by 53k • written 2.9 years ago by ▴ 10
0
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17
replies
3.1k
views
How to check linear model
modalmatrix limma R linear
2.9 years ago Jitendra ▴ 10
6
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11
replies
2.5k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
2.9 years ago mohammedtoufiq91 ▴ 10
0
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1
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1.2k
views
Differential expression analysis with global differences among samples (tissues)
DESeq2 qsmooth edgeR limma
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
5
votes
2
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1.4k
views
Sva and batch effect
limma BatchEffect sva
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
1
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3
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1.8k
views
Limma-voom with inverse probability weights (similar to sample weights)
limma limma-voom StatisticalMethod
updated 3.0 years ago by 53k • written 3.0 years ago by ▴ 10
2
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4
replies
1.9k
views
Reproducibility using limma for DE Analysis
limma seed DifferentialRegulation
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
4
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1
reply
2.2k
views
on which data type limma::removeBatchEffect can be applyed?
batch limma
updated 3.0 years ago by ★ 5.0k • written 3.0 years ago by ▴ 50
3
votes
5
replies
1.8k
views
Design for DE analysis in tidybulk
DESeq2 designmatrix edgeR limma tidybulk
updated 3.0 years ago by 43k • written 3.0 years ago by ▴ 10
0
votes
1
reply
1.7k
views
limma: decideTests
affy limma affy limma
updated 3.0 years ago by 53k • written 18.1 years ago by ▴ 270
0
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1
reply
741
views
NAs in some genes in topTable output
limma topTable
updated 3.0 years ago by 53k • written 3.0 years ago by ▴ 10
0
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1
reply
1.2k
views
limma on spectral data
limma Metabolomics DifferentialExpression POMA
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
1
vote
2
replies
5.0k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
3
votes
4
replies
2.4k
views
Processing data with voom "expression values" and "weights"
limma voom
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
2
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2
replies
1.3k
views
Estimating Fold-Changes of Lowly Expressed Genes
limma
3.0 years ago vm ▴ 30
0
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2
replies
1.8k
views
Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
3.0 years ago dqt • 0
0
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1
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1.1k
views
Limma: how to make a table of logFC of certain genes (I need to define logFC of 62 genes specific for the cells of interest)
DifferentialExpression limma R TissueMicroarrayData
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
3
votes
3
replies
2.6k
views
Limma repeated-measures model: Partial NA coefficients
Proteomics limma repeated-measures
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
0
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1
reply
1.0k
views
Assigning the name of top 100 DE transcripts/genes to Volcano plot
limma DEGreport Volcanoplot
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
1
vote
1
reply
1.1k
views
Alternatives to Voom in experiments without replicate
limma edgeR Voom
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
1
vote
1
reply
1.4k
views
Extracting the tophits from limma Volcanoplot and issue with geneIDs
limma edgeR Glimma
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
2
votes
1
reply
1.2k
views
limma: R-squared for time-series data
limma
updated 3.1 years ago by 53k • written 3.1 years ago by ★ 5.0k
0
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0
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547
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A problem with Experimental Design for Limma
limma RNASeq
3.1 years ago ToReality • 0
0
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0
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830
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normFactors or calcNormFactors (computing the normalization or scaling factors)
limma edgeR csaw
3.1 years ago Bogdan ▴ 670
3
votes
6
replies
1.9k
views
Question about making Contrasts for comparisons and assignment of values
edgeR contrasts limma design model.matrix
3.1 years ago mohammedtoufiq91 ▴ 10
6
votes
6
replies
3.1k
views
limma plotMDS - logFC inverted?
limma MultidimensionalScaling
updated 16 months ago by 68k • written 3.1 years ago by • 0
1
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1
reply
738
views
Limma, Log2FC and pvalue changing depending on the order of the samples.
limma
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
4
votes
6
replies
1.9k
views
Question on creating right design matrix in edgeR
R designmatrix edgeR limma model.matrix
3.1 years ago Abdul ▴ 20
1
vote
3
replies
1.0k
views
Limma-voom - Timepoint by timepoint comparison in timecourse experiment
limma
written 3.1 years ago by ▴ 30
1
vote
2
replies
1.3k
views
Extracting specific comparisons after fitting model in EdgeR
edgeR limma design RNASeq model.matrix
3.1 years ago mohammedtoufiq91 ▴ 10
4
votes
8
replies
3.6k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 2.7 years ago by 53k • written 3.1 years ago by ▴ 20
1
vote
2
replies
1.3k
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
3.1 years ago mohammedtoufiq91 ▴ 10
1
vote
12
replies
3.9k
views
normalization of ChIP-seq data by using the spike-ins or by using total library sizes
DESeq2 edgeR limma
updated 3.1 years ago by 43k • written 3.2 years ago by ▴ 670
6
votes
6
replies
2.3k
views
Too many differentially expressed miRNA with limma
limma miRNA Microarray
3.2 years ago Sara ▴ 20
0
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4
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1.4k
views
Time course experiment with limma voom
limma
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
0
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5
replies
1.8k
views
Limma: posterior distribution of error variance
limma
3.2 years ago gabriel.hoffman ▴ 170
3
votes
6
replies
3.6k
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
3.2 years ago Sara • 0
3
votes
5
replies
2.4k
views
limma-trend vs. limma-voom theoretical difference
limma limma-trend limma-voom
updated 2.0 years ago by ▴ 30 • written 3.2 years ago by • 0
1
vote
3
replies
1.2k
views
Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
3
votes
7
replies
2.9k
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
0
votes
6
replies
5.2k
views
limma vs lme4: definition of "random effects"
limma lme4 mixed
3.2 years ago leandro • 0
0
votes
3
replies
982
views
limma manual typo
limma
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
1
vote
3
replies
1.6k
views
Proteomics-time series with repeated measures
Proteomics limma repeatedmeasures TimeSeriesExperiment
3.2 years ago proteome_AO • 0
0
votes
17
replies
4.5k
views
Advice for the analysis of microarray data with limma
Microarray MicroarrayData limma
updated 3.0 years ago by 53k • written 3.2 years ago by • 0
1
vote
2
replies
1.1k
views
Can fry() be used on infinium methylation array data to call differential methylation?
limma infinium fry
3.3 years ago mark.ziemann • 0
1
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1
reply
3.6k
views
installation of BioC packages on Mac M1 Monterrey OS
limma Bioconductor edgeR
3.3 years ago Bogdan ▴ 670
4,230 results • Page 6 of 85
Recent ...
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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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