Showing : Limma • reset
6
votes
11
replies
2.4k
views
Error in running Dispersion estimation analysis in EdgeR
edgeR DifferentialExpression limma design RNASeq
2.7 years ago mohammedtoufiq91 ▴ 10
0
votes
1
reply
1.2k
views
Differential expression analysis with global differences among samples (tissues)
DESeq2 qsmooth edgeR limma
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
5
votes
2
replies
1.3k
views
Sva and batch effect
limma BatchEffect sva
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
1
vote
3
replies
1.7k
views
Limma-voom with inverse probability weights (similar to sample weights)
limma limma-voom StatisticalMethod
updated 2.8 years ago by 53k • written 2.8 years ago by ▴ 10
2
votes
4
replies
1.8k
views
Reproducibility using limma for DE Analysis
limma seed DifferentialRegulation
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
4
votes
1
reply
2.1k
views
on which data type limma::removeBatchEffect can be applyed?
batch limma
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by ▴ 50
3
votes
5
replies
1.7k
views
Design for DE analysis in tidybulk
DESeq2 designmatrix edgeR limma tidybulk
updated 2.8 years ago by 43k • written 2.8 years ago by ▴ 10
0
votes
1
reply
1.6k
views
limma: decideTests
affy limma affy limma
updated 2.8 years ago by 53k • written 17.9 years ago by ▴ 270
0
votes
1
reply
684
views
NAs in some genes in topTable output
limma topTable
updated 2.8 years ago by 53k • written 2.8 years ago by ▴ 10
0
votes
1
reply
1.2k
views
limma on spectral data
limma Metabolomics DifferentialExpression POMA
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
1
vote
2
replies
4.7k
views
R: Confused about Limma R package output being LogFC or Log2FC
limma R ExpressionData
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
3
votes
4
replies
2.2k
views
Processing data with voom "expression values" and "weights"
limma voom
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
2
votes
2
replies
1.2k
views
Estimating Fold-Changes of Lowly Expressed Genes
limma
2.8 years ago vm ▴ 30
0
votes
2
replies
1.7k
views
Remove batch effect between microarray data
Microarray DifferentialExpression limma MicroarrayData removebatcheffect
2.8 years ago dqt • 0
0
votes
1
reply
1.0k
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 2.8 years ago by 53k • written 2.8 years ago by • 0
3
votes
3
replies
2.5k
views
Limma repeated-measures model: Partial NA coefficients
Proteomics limma repeated-measures
updated 2.8 years ago by 53k • written 2.9 years ago by • 0
0
votes
1
reply
973
views
Assigning the name of top 100 DE transcripts/genes to Volcano plot
limma DEGreport Volcanoplot
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
1
vote
1
reply
1.0k
views
Alternatives to Voom in experiments without replicate
limma edgeR Voom
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
1
vote
1
reply
1.3k
views
Extracting the tophits from limma Volcanoplot and issue with geneIDs
limma edgeR Glimma
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
2
votes
1
reply
1.1k
views
limma: R-squared for time-series data
limma
updated 2.9 years ago by 53k • written 2.9 years ago by ★ 5.0k
0
votes
0
replies
510
views
A problem with Experimental Design for Limma
limma RNASeq
2.9 years ago ToReality • 0
0
votes
0
replies
792
views
normFactors or calcNormFactors (computing the normalization or scaling factors)
limma edgeR csaw
2.9 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
2.9 years ago mohammedtoufiq91 ▴ 10
6
votes
6
replies
3.0k
views
limma plotMDS - logFC inverted?
limma MultidimensionalScaling
updated 14 months ago by 68k • written 2.9 years ago by • 0
1
vote
1
reply
717
views
Limma, Log2FC and pvalue changing depending on the order of the samples.
limma
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
4
votes
6
replies
1.8k
views
Question on creating right design matrix in edgeR
R designmatrix edgeR limma model.matrix
2.9 years ago Abdul ▴ 20
1
vote
3
replies
927
views
Limma-voom - Timepoint by timepoint comparison in timecourse experiment
limma
written 2.9 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
2.9 years ago mohammedtoufiq91 ▴ 10
4
votes
8
replies
3.4k
views
Can we use rlog or vst data values in limma for differential expression analysis?
DESeq2 limma Normalization R
updated 2.5 years ago by 53k • written 2.9 years ago by ▴ 20
1
vote
2
replies
1.2k
views
Does negative corfit$consensus cause issues while fitting a model in limma
limma R design model.matrix
2.9 years ago mohammedtoufiq91 ▴ 10
1
vote
12
replies
3.7k
views
normalization of ChIP-seq data by using the spike-ins or by using total library sizes
DESeq2 edgeR limma
updated 2.9 years ago by 43k • written 3.0 years ago by ▴ 670
6
votes
6
replies
2.2k
views
Too many differentially expressed miRNA with limma
limma miRNA Microarray
3.0 years ago Sara ▴ 20
0
votes
4
replies
1.4k
views
Time course experiment with limma voom
limma
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
0
votes
5
replies
1.6k
views
Limma: posterior distribution of error variance
limma
3.0 years ago gabriel.hoffman ▴ 170
3
votes
6
replies
3.4k
views
Limma: log2 of TMM values for RNA-Seq Analysis and PlotMDS()?
Log2 edgeR RNA limma Normalization
3.0 years ago Sara • 0
3
votes
5
replies
2.2k
views
limma-trend vs. limma-voom theoretical difference
limma limma-trend limma-voom
updated 22 months ago by ▴ 30 • written 3.0 years ago by • 0
1
vote
3
replies
1.1k
views
Limma F-statistic identical for different comparison, why?
limma F-statistic contrasts
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
3
votes
7
replies
2.8k
views
How to visaulize RNAseq data with edgeR, limma, ...?
r rnaseq DifferentialExpression limma edger
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
0
votes
6
replies
4.7k
views
limma vs lme4: definition of "random effects"
limma lme4 mixed
3.0 years ago leandro • 0
0
votes
3
replies
946
views
limma manual typo
limma
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
1
vote
3
replies
1.5k
views
Proteomics-time series with repeated measures
Proteomics limma repeatedmeasures TimeSeriesExperiment
3.0 years ago proteome_AO • 0
0
votes
17
replies
4.1k
views
Advice for the analysis of microarray data with limma
Microarray MicroarrayData limma
updated 2.8 years ago by 53k • written 3.1 years ago by • 0
1
vote
2
replies
997
views
Can fry() be used on infinium methylation array data to call differential methylation?
limma infinium fry
3.1 years ago mark.ziemann • 0
1
vote
1
reply
3.4k
views
installation of BioC packages on Mac M1 Monterrey OS
limma Bioconductor edgeR
3.1 years ago Bogdan ▴ 670
0
votes
1
reply
2.4k
views
bigwig to counts
DESeq2 edgeR bigwig limma
3.1 years ago • updated 2.8 years ago Bogdan ▴ 670
1
vote
1
reply
1.3k
views
Weird distribution of p-values, with no significant adjusted p-values?
fdr limmaGUI p-values limma
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
0
votes
7
replies
2.0k
views
Help with differential gene expression using Agilent Microarray data (from GEO database)
limma Paireddata DifferentialExpression
updated 3.0 years ago by 68k • written 3.1 years ago by • 0
1
vote
2
replies
1.7k
views
Limma adj.p.value the same for many different p.values
limmaGUI limma adj.p.value StatisticalMethod
3.1 years ago walkerrh95 • 0
3
votes
7
replies
2.9k
views
Different results between Limma and DESEQ2 for Differential Expression Analysis
DESeq2 limma
updated 3.1 years ago by ★ 1.4k • written 3.1 years ago by ▴ 50
5
votes
8
replies
3.0k
views
Question on performing filtering by gene expression on a normalized matrix in limma?
expression R filtering limma
3.1 years ago • updated 2.9 years ago mohammedtoufiq91 ▴ 10
4,225 results • Page 6 of 85
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Comment: Save the Date: BioC2026 by eja.gsssssswwse.r.m • 0
Que notícia incrivel sobre o BioC2026 Para quem gosta de aproveitar o conteudo online, também e possvel Baixar [snaptube versão antiga][1] …
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Keeping up with Ensembls latest release ensures access to cutting-edge genomic information. For those balancing research and leisure, a mob…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
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Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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