Showing : Limma • reset
15
votes
23
replies
4.2k
views
The difference when using Limma compare between 3 conditions vs 2 conditions
limma
12 months ago • updated 11 months ago Chris ▴ 20
15
votes
17
replies
2.8k
views
Why p value inconsistent when using different number of pathway score?
limma
12 months ago • updated 11 months ago Chris ▴ 20
4
votes
14
replies
2.1k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign limma pairedsamples
updated 8 months ago by 52k • written 9 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
2
votes
12
replies
2.2k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
6 months ago • updated 5 months ago john • 0
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
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 4 months ago by ▴ 10
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
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
0
votes
9
replies
1.2k
views
Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 4 months ago by 68k • written 4 months ago by • 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
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
1
vote
8
replies
1.8k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 5 months ago by • 0
1
vote
6
replies
945
views
limma and Syntactically Invalid Factor Values
limma
updated 9 months ago by 52k • written 9 months ago by ★ 1.6k
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
4
votes
6
replies
1.4k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
6 months ago • updated 5 months ago altintas.ali • 0
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
8
votes
6
replies
1.9k
views
Unbalanced experiment with multiple samples from each patient.
limma
updated 7 weeks ago by • 0 • written 7.3 years ago by ▴ 10
2
votes
5
replies
838
views
Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 9 months ago by 68k • written 9 months ago by • 0
0
votes
5
replies
874
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
5 months ago • updated 4 months ago abadgerw • 0
6
votes
5
replies
753
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 3 months ago by 68k • written 3 months ago by • 0
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
5
votes
5
replies
1.3k
views
Limma with covariates
limma
written 10 months ago by ▴ 20
1
vote
5
replies
1.1k
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
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 4.5 years ago by ▴ 10
2
votes
5
replies
510
views
Differential variability modelling with vst() expression
limma DESeq2
written 3 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
5
votes
4
replies
735
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 6 months ago by ★ 4.8k • written 6 months ago by • 0
4
votes
4
replies
841
views
Warning message when running limma with covariates
limma
10 months ago • updated 3 months ago Chris ▴ 20
3
votes
4
replies
767
views
Help with error using camera() in limma
CAMERA limma
11 months ago Chris ▴ 20
2
votes
4
replies
977
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
8 weeks ago • updated 7 weeks ago svlachavas ▴ 840
3
votes
4
replies
885
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
5 months ago dseauer • 0
3
votes
4
replies
900
views
using limma trend workflow in CAMERA
CAMERA limma
8 months ago • updated 7 months ago Jay • 0
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
0
votes
3
replies
2.1k
views
RE:proper pooling design
Microarray Normalization affy makecdfenv limma marray Microarray Normalization affy limma
updated 9 days ago by • 0 • written 21.3 years ago by ▴ 70
0
votes
3
replies
1.8k
views
Limma, eBayes different sample size of groups and adjustment
limma limma
updated 11 months ago by • 0 • written 14.0 years ago by ▴ 10
8
votes
3
replies
4.5k
views
Appropriate ways to filter counts data for voom/limma
limma edger sequencing
written 8.7 years ago by ▴ 10
2
votes
3
replies
684
views
Explanation for ROAST results
CAMERA limma
updated 28 days ago by 52k • written 28 days 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
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 10 weeks ago by • 0 • written 3.7 years ago by • 0
3
votes
3
replies
789
views
One-sided tests with CAMERA-PR
CAMERA limma
updated 8 months ago by 52k • written 8 months ago by ▴ 10
5
votes
3
replies
844
views
Limma comparing gene expression between base line and one treatment
limma
updated 9 months ago by 68k • written 9 months ago by • 0
11
votes
3
replies
2.6k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
written 16 months ago by • 0
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
4
votes
3
replies
968
views
Analysis of 2*4 factorial design
limma
updated 5 months ago by 52k • written 6 months ago by • 0
1
vote
3
replies
568
views
Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 5 months ago by • 0
2
votes
3
replies
1.3k
views
how to use `arrayWeightsQuick()`?
limma
updated 12 days ago by 52k • written 13 days ago by • 0
0
votes
3
replies
723
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 8 months ago by 52k • written 8 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 5 months ago by • 0
3
votes
3
replies
472
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
6 months ago Guido Hooiveld ★ 4.1k
50 results • Page 1 of 1
Recent ...
Replies
Answer: EuroBioC2024 abstract submission is open! by Ali • 0
[Promo products][1] are a smart way to boost visibility, especially with exciting updates like *News: EuroBioC2024 abstract submission is o…
Answer: ROAST for small sets by Gordon Smyth 52k
The p-values from `mroast` will be the same (up to sampling variability associated with random rotations) regardless of whether you test al…
Comment: FlowSOM library requires igraph but igraph does not install by Szabolcs • 0
The R/igraph Installation FAQ covers most issues: https://r.igraph.org/articles/installation-troubleshooting.html
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much for the vis suggestion!
Comment: edgeR::cpm() results in negative values from raw counts of 0 by Kinnary ▴ 20
Thank you very much - I appreciate the mathematical explanation and link to Dr. Phipson's thesis!
Votes
Answer: ROAST for small sets
Answer: ROAST for small sets
A: conceptual question about FDR, FDR adjusted p-value and q-value
Comment: edgeR::cpm() results in negative values from raw counts of 0
Comment: edgeR::cpm() results in negative values from raw counts of 0
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