Showing : Limma • reset
1
vote
3
replies
787
views
Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 11 months ago by • 0
0
votes
2
replies
412
views
List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
11 months ago giulia.gentile ▴ 10
4
votes
2
replies
1.3k
views
Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 11 months ago by 53k • written 11 months ago by ▴ 60
1
vote
2
replies
498
views
Limma Interaction Effect with Covariates
limma DMRcate
11 months ago kitzhu • 0
2
votes
3
replies
1.3k
views
[How to construct a model.matrix ]
limma modelmatrix
updated 11 months ago by 53k • written 11 months ago by • 0
3
votes
4
replies
1.2k
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
11 months ago dseauer • 0
1
vote
3
replies
849
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
12 months ago • updated 11 months ago abadgerw • 0
0
votes
5
replies
1.2k
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
12 months ago • updated 11 months ago abadgerw • 0
1
vote
8
replies
2.4k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 12 months ago by • 0
1
vote
2
replies
1.4k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
12 months ago Ai • 0
3
votes
3
replies
1.5k
views
Robust way of dealing with low number of samples for Differential Gene Expression
limma edgeR DESeq2 MAST
written 12 months ago by • 0
4
votes
3
replies
1.2k
views
Analysis of 2*4 factorial design
limma
updated 12 months ago by 53k • written 12 months ago by • 0
2
votes
12
replies
2.7k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
12 months ago • updated 11 months ago john • 0
4
votes
6
replies
1.9k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 12 months ago by 53k • written 12 months ago by • 0
4
votes
6
replies
1.8k
views
Zero intra-block correlation in RRBS analysis using voomLmFit with block
limma duplicateCorrelation edgeR modelMatrixMeth voomLmFit
12 months ago altintas.ali • 0
2
votes
2
replies
853
views
Automatically generate contrasts from a model matrix / formula
limma
updated 12 months ago by ★ 5.0k • written 12 months ago by ▴ 10
3
votes
3
replies
725
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
13 months ago • updated 12 months ago Guido Hooiveld ★ 4.1k
0
votes
3
replies
723
views
Need help interpreting heatmaps from limma
limma
written 13 months ago by • 0
2
votes
1
reply
2.0k
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 13 months ago by 68k • written 13 months ago by ▴ 10
5
votes
4
replies
976
views
How to control batch effect if Group and batch are same?
limma DESeq2 BatchEffect
updated 13 months ago by ★ 5.0k • written 13 months ago by • 0
1
vote
2
replies
861
views
Poor dispersion fit in DESeq2
limma DESeq2 RNASeq edgeR
updated 13 months ago by 43k • written 13 months ago by ▴ 10
0
votes
0
replies
459
views
Assistance with Bulk RNA-seq Data Analysis Including Random Effect (`duplicateCorrelation` from `limma`)
limma RNAseq123
13 months ago tim.meese • 0
0
votes
2
replies
774
views
EdgeR - Apparent Wrong Direction of logFC with Low Count Data
limma edgeR
updated 13 months ago by 53k • written 13 months ago by • 0
0
votes
2
replies
700
views
Question on performing ANOVA-like analysis using limma
limma
updated 13 months ago by 53k • written 13 months ago by • 0
17
votes
9
replies
8.2k
views
How to use removeBatchEffect for removing effect of multiple confounding variables
limma removebatcheffect deseq2
updated 13 months ago by 68k • written 9.4 years ago by ▴ 10
2
votes
1
reply
722
views
Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjusting for Covariates?
MethylationArray EpigeneticsWorkflow limma Regression
updated 14 months ago by 68k • written 14 months ago by ▴ 20
0
votes
1
reply
2.1k
views
Unable to install/use limma
limma Bioconductor
updated 14 months ago by 68k • written 14 months ago by • 0
3
votes
3
replies
934
views
voom does not seem to properly correct for library size
limma
updated 14 months ago by 53k • written 14 months ago by ★ 5.0k
1
vote
5
replies
1.4k
views
RNASeq normlization for samples with global shift in gene expression
qsmooth DESeq2 limma Normalization
updated 14 months ago by 53k • written 14 months ago by • 0
0
votes
3
replies
943
views
Differential expression analysis in time course experiments with DESeq2
DESeq2 limma DifferentialExpression
updated 14 months ago by 53k • written 14 months ago by • 0
3
votes
4
replies
1.2k
views
using limma trend workflow in CAMERA
CAMERA limma
14 months ago Jiahao Tian • 0
3
votes
3
replies
964
views
One-sided tests with CAMERA-PR
CAMERA limma
updated 15 months ago by 53k • written 15 months ago by ▴ 10
1
vote
6
replies
1.2k
views
limma and Syntactically Invalid Factor Values
limma
updated 15 months ago by 53k • written 15 months ago by ★ 1.6k
1
vote
1
reply
1.0k
views
DEG Analysis using Limma on DSP GeoMx Data: Handling Multiple ROIs per Core
limma DSP GeomxTools
15 months ago Bioinformagician • 0
5
votes
3
replies
1.0k
views
Limma comparing gene expression between base line and one treatment
limma
updated 15 months ago by 68k • written 15 months ago by • 0
0
votes
1
reply
1.1k
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
2
votes
5
replies
1.1k
views
Limma - 0 downreg and upreg values
GeoMx limma DifferentialExpression
updated 15 months ago by 68k • written 15 months ago by • 0
4
votes
14
replies
2.6k
views
LIMMA 2x2 Factorial Design with Paired Samples
factorialdesign limma pairedsamples
updated 15 months ago by 53k • written 16 months ago by • 0
3
votes
4
replies
1.2k
views
Differences in Limma and Dreamlet random effects from confounded dataset
limma dreamlet
16 months ago jcollier • 0
4
votes
4
replies
1.7k
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
16 months ago sukeshinik5 ▴ 20
0
votes
1
reply
554
views
Deseq2 design matrix
DESeq2 Designmatrix limma
updated 16 months ago by 68k • written 16 months ago by • 0
4
votes
4
replies
1.1k
views
Warning message when running limma with covariates
limma
16 months ago • updated 10 months ago Chris ▴ 20
0
votes
8
replies
2.2k
views
limma comparison for small sample size and how to get covariance matrix
covariancematrix limma
16 months ago jiachengd • 0
5
votes
5
replies
1.7k
views
Limma with covariates
limma
written 16 months ago by ▴ 20
3
votes
13
replies
2.0k
views
Limma model.matrix design with batch effect and different life stages proportion estimates
DeconRNASeq limma
updated 17 months ago by • 0 • written 17 months ago by • 0
3
votes
2
replies
1.2k
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
17 months ago mohammedtoufiq91 ▴ 10
1
vote
2
replies
791
views
Subsetting RNAseq data | voomaByGroup()
limma
17 months ago Anna • 0
1
vote
2
replies
1.0k
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
18 months ago Dylan.Sheerin • 0
2
votes
2
replies
1.2k
views
error in limma , contrast.matrix Number of rows of contrast matrix must match number of coefficients in fit
limma
18 months ago user_bioinfo • 0
3
votes
10
replies
1.9k
views
Extremely small p-values using Limma for proteomic data
Proteomics limma
updated 18 months ago by 68k • written 18 months ago by • 0
4,225 results • Page 2 of 85
Recent ...
Replies
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 bioinffun, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to …
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…
Answer: featureCounts -L: high unassigned:mapq fraction by Kevin Blighe ★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Answer: Streamlining the computing time for MiloDE p-value correction in large dataset? by Kevin Blighe ★ 4.0k
Hi Joseph, I agree with ATpoint's suggestion that pseudobulk aggregation (e.g., via aggregateData in scran or similar) would likely be f…
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
Awards • All
Scholar to shepherl 4.2k
Scholar to James W. MacDonald 68k
Popular Question to Daniel Cameron ▴ 40
Popular Question to Peter Hickey ▴ 760
Popular Question to edward.esiribloom • 0
Locations • All
The city by the bay, 1 hour ago
United States, 2 hours ago
WEHI, Melbourne, Australia, 3 hours ago
United States, 5 hours ago
The Cave, 181 Longwood Avenue, Boston, USA, 5 hours ago
Traffic: 1177 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6