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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
Gordon Smyth
53k • written 2.7 years ago by
Gregory
• 0
5
votes
2
replies
1.3k
views
Sva and batch effect
limma
BatchEffect
sva
updated 2.8 years ago by
Gordon Smyth
53k • written 2.8 years ago by
Lenny186
• 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
Gordon Smyth
53k • written 2.8 years ago by
jay
▴ 10
2
votes
4
replies
1.8k
views
Reproducibility using limma for DE Analysis
limma
seed
DifferentialRegulation
updated 2.8 years ago by
Gordon Smyth
53k • written 2.8 years ago by
TSauer
• 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
ATpoint
★ 5.0k • written 2.8 years ago by
luca.s
▴ 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
Michael Love
43k • written 2.8 years ago by
aditya.m
▴ 10
0
votes
1
reply
1.6k
views
limma: decideTests
affy
limma
affy
limma
updated 2.8 years ago by
Gordon Smyth
53k • written 17.9 years ago by
Al Ivens
▴ 270
0
votes
1
reply
684
views
NAs in some genes in topTable output
limma
topTable
updated 2.8 years ago by
Gordon Smyth
53k • written 2.8 years ago by
thkapell
▴ 10
0
votes
1
reply
1.2k
views
limma on spectral data
limma
Metabolomics
DifferentialExpression
POMA
updated 2.8 years ago by
Gordon Smyth
53k • written 2.8 years ago by
wiscoyogi
• 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
Gordon Smyth
53k • written 2.8 years ago by
Keith
• 0
3
votes
4
replies
2.2k
views
Processing data with voom "expression values" and "weights"
limma
voom
updated 2.8 years ago by
Gordon Smyth
53k • written 2.8 years ago by
Edmond
• 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
Gordon Smyth
53k • written 2.8 years ago by
Элина
• 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
Gordon Smyth
53k • written 2.9 years ago by
Luís C.
• 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
Gordon Smyth
53k • written 2.9 years ago by
Mohammad
• 0
1
vote
1
reply
1.0k
views
Alternatives to Voom in experiments without replicate
limma
edgeR
Voom
updated 2.9 years ago by
Gordon Smyth
53k • written 2.9 years ago by
Mohammad
• 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
Gordon Smyth
53k • written 2.9 years ago by
Mohammad
• 0
2
votes
1
reply
1.1k
views
limma: R-squared for time-series data
limma
updated 2.9 years ago by
Gordon Smyth
53k • written 2.9 years ago by
ATpoint
★ 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
James W. MacDonald
68k • written 2.9 years ago by
Katharina
• 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
Gordon Smyth
53k • written 2.9 years ago by
eiudkann
• 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
rina
▴ 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
Gordon Smyth
53k • written 2.9 years ago by
Sabiha
▴ 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
Michael Love
43k • written 3.0 years ago by
Bogdan
▴ 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
Gordon Smyth
53k • written 3.0 years ago by
mahes.muniandy
• 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
floriandeckert
▴ 30 • written 3.0 years ago by
hainct
• 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
Gordon Smyth
53k • written 3.0 years ago by
jeltje.van.baren
• 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
Gordon Smyth
53k • written 3.0 years ago by
jirkamanuel.petersen
• 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
Gordon Smyth
53k • written 3.0 years ago by
jeltje.van.baren
• 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
Gordon Smyth
53k • written 3.1 years ago by
Sam
• 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
James W. MacDonald
68k • written 3.1 years ago by
seahorsebox828
• 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
James W. MacDonald
68k • written 3.1 years ago by
r02eb20
• 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
swbarnes2
★ 1.4k • written 3.1 years ago by
Bine
▴ 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] …
Comment: Ensembl 115 has been released!
by
eja.gsssssswwse.r.m
• 0
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…
Answer: gene Set with high AUC score but no cells assigned to cell type
by
Kevin Blighe
★ 4.0k
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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