Showing : Limma • reset
34
votes
11
replies
43k
views
Differential expression of FPKM from RNA-seq data using limma and voom()
limma
written 11.4 years ago by ▴ 260
17
votes
9
replies
7.6k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 7 months ago by 68k • written 8.9 years ago by ▴ 10
8
votes
3
replies
4.6k
views
Appropriate ways to filter counts data for voom/limma
limma edger sequencing
written 8.7 years ago by ▴ 10
15
votes
23
replies
4.3k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
13 months ago • updated 12 months ago Chris ▴ 20
6
votes
10
replies
2.9k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 4 months ago by ★ 4.8k • written 5 months ago by ▴ 10
15
votes
17
replies
2.8k
views
Why p value inconsistent when using different number of pathway score?
limma
12 months ago Chris ▴ 20
11
votes
3
replies
2.7k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
written 17 months ago by • 0
6
votes
6
replies
2.6k
views
limma plotMDS - logFC inverted?
limma MultidimensionalScaling
updated 7 months ago by 68k • written 2.4 years ago by • 0
2
votes
12
replies
2.2k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
6 months ago • updated 5 months ago john • 0
3
votes
2
replies
2.1k
views
Multi-level design RRBS analysis with voomLmFit
edgeR voomLmFit limma duplicateCorrelation voom
updated 6 months ago by 52k • written 3.4 years ago by • 0
4
votes
14
replies
2.1k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign limma pairedsamples
updated 9 months ago by 52k • written 9 months ago by • 0
0
votes
3
replies
2.1k
views
RE:proper pooling design
Microarray Normalization affy makecdfenv limma marray Microarray Normalization affy limma
updated 16 days ago by • 0 • written 21.3 years ago by ▴ 70
3
votes
1
reply
2.1k
views
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
Limma ebayes bayesian ls
updated 11 months ago by 52k • written 6.6 years ago by ▴ 10
9
votes
6
replies
2.0k
views
Unbalanced experiment with multiple samples from each patient.
limma
updated 8 weeks ago by • 0 • written 7.4 years ago by ▴ 10
1
vote
8
replies
1.9k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 5 months ago by • 0
0
votes
8
replies
1.9k
views
limma comparison for small sample size and how to get covariance matrix
covariancematrix limma
10 months ago • updated 9 months ago jiachengd • 0
0
votes
3
replies
1.8k
views
Limma, eBayes different sample size of groups and adjustment
limma limma
updated 12 months ago by • 0 • written 14.0 years ago by ▴ 10
2
votes
1
reply
1.8k
views
Removing Effect of Covariate in Only a Subset of Samples in a Model Containing All Samples Loses Full Rank if Factor but not Numerical
limma
updated 6 months ago by 68k • written 6 months ago by ▴ 10
0
votes
3
replies
1.8k
views
Why the order of sample names in the beta matrix affect the analysis results of Champ.DMP? What should I do?
ChAMP limma Bioconductor ChAMPdata
updated 11 weeks ago by • 0 • written 3.7 years ago by • 0
2
votes
5
replies
1.7k
views
How should I handle read counts derived from SGSeq when they were passed to limma/edgeR
SGSeq limma edgeR
updated 7 months ago by • 0 • written 4.6 years ago by ▴ 10
4
votes
6
replies
1.7k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 6 months ago by 52k • written 6 months ago by • 0
3
votes
13
replies
1.6k
views
Limma model.matrix design with batch effect and different life stages proportion estimates
DeconRNASeq limma
updated 10 months ago by • 0 • written 10 months ago by • 0
0
votes
1
reply
1.5k
views
Unable to install/use limma
limma Bioconductor
updated 7 months ago by 68k • written 7 months ago by • 0
4
votes
6
replies
1.5k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
6 months ago altintas.ali • 0
1
vote
1
reply
1.4k
views
A question about paired data and how to set up the designmatrix in LIMMA
limma affydata
19.8 years ago • updated 9 months ago Gordon Smyth 52k
3
votes
10
replies
1.4k
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 11 months ago by 68k • written 11 months ago by • 0
2
votes
3
replies
1.4k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 4 months ago by 68k • written 4 months ago by ▴ 10
3
votes
5
replies
1.4k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 3 months ago by 68k • written 3 months ago by ▴ 10
4
votes
4
replies
1.4k
views
Using both voom and removeBatchEffect, will they double adjust the data or is it the right way to perform this
limma adjustment voom removeBatchEffect covariates
10 months ago sukeshinik5 ▴ 20
2
votes
3
replies
1.4k
views
how to use `arrayWeightsQuick()`?
limma
updated 19 days ago by 52k • written 20 days ago by • 0
2
votes
2
replies
1.3k
views
limma for gene expression analysis with big and unbalanced sample size
limma microarray statistics
updated 12 months ago by • 0 • written 8.9 years ago by • 0
5
votes
3
replies
1.3k
views
Log-cpm values from limma
limma edgeR RNASeq
updated 11 months ago by 52k • written 12 months ago by • 0
5
votes
5
replies
1.3k
views
Limma with covariates
limma
written 10 months ago by ▴ 20
2
votes
2
replies
1.2k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 4 weeks ago by ★ 4.8k • written 5 weeks ago by • 0
0
votes
9
replies
1.2k
views
Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 4 months ago by 68k • written 5 months ago by • 0
3
votes
3
replies
1.2k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 6 months ago by • 0
1
vote
5
replies
1.2k
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 8 months ago by 52k • written 8 months ago by • 0
2
votes
2
replies
1.1k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
7 weeks ago • updated 6 weeks ago Elizabeth • 0
1
vote
2
replies
1.1k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
5 months ago Ai • 0
1
vote
9
replies
1.1k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 4 months ago by ▴ 30
2
votes
3
replies
1.1k
views
[How to construct a model.matrix ]
limma modelmatrix
updated 5 months ago by 52k • written 5 months ago by • 0
3
votes
4
replies
1.0k
views
Differences in Limma and Dreamlet random effects from confounded dataset
limma dreamlet
9 months ago jcollier • 0
2
votes
2
replies
1000
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
11 months ago user_bioinfo • 0
2
votes
4
replies
998
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
9 weeks ago • updated 8 weeks ago svlachavas ▴ 840
4
votes
3
replies
980
views
Analysis of 2*4 factorial design
limma
updated 6 months ago by 52k • written 6 months ago by • 0
1
vote
6
replies
958
views
limma and Syntactically Invalid Factor Values
limma
updated 9 months ago by 52k • written 9 months ago by ★ 1.6k
3
votes
2
replies
925
views
limma Intercept vs No-intercept models completely changing DMR results?
limma DMRcate MethylationArray EPICV2
updated 11 months ago by 52k • written 12 months ago by • 0
3
votes
4
replies
919
views
using limma trend workflow in CAMERA
CAMERA limma
8 months ago Jay • 0
0
votes
1
reply
915
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 9 months ago by ★ 4.8k • written 9 months ago by • 0
3
votes
2
replies
906
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
11 months ago mohammedtoufiq91 ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Cannot extract size factor from DESeq2 analysis by s.malik • 0
Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…
Comment: Design formula for circadian time-course data for vst() function by Vishnu • 0
Thank you so much for your reply.
Comment: Analyzing TnSeq data with DESeq2 by Tom • 0
[Doncaster Locksmith][1] delivers trusted, efficient security services tailored to your needs. Analyzing TnSeq data with DESeq2 may uncover…
Answer: Design formula for circadian time-course data for vst() function by ATpoint ★ 4.8k
This was asked before: https://support.bioconductor.org/p/9148734/#9148812 Take-home message is that influence is minor, as you see your…
Comment: Filtering after DESeq by caroline.zanchi • 0
... I did it. It does filter out quite a bit of genes : ``` keep <- filterByExpr(dds, group="host_treatment_generation",min.count = 10, mi…
Votes
Answer: CluserProfiler message "No gene can be mapped"
A: Minfi issue: return code from pthread_create() is 22
Comment: Filtering after DESeq
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
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