Showing : limma • reset
2
votes
6
replies
1.2k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
updated 7 hours ago by 52k • written 20 days ago by • 0
11
votes
4
replies
3.3k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
updated 2 days ago by 52k • written 17 months ago by • 0
5
votes
7
replies
2.8k
views
limma correction for tumor purity
limma
11 days ago • updated 5 days ago gabriella.jacobson-eisenberg ▴ 20
2
votes
5
replies
875
views
Dealing with heteroscedascity in limma
limma splines Proteomics
written 11 days ago by • 0
0
votes
3
replies
691
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 5 weeks ago by ▴ 10
4
votes
0
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3.2k
views
Evidence-based guidelines for use the method="robust" option in lmFit
Microarray Normalization Bayesian Regression Cancer limma Microarray Normalization Cancer
updated 11 days ago by • 0 • written 14.0 years ago by ★ 2.0k
2
votes
4
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1.6k
views
how to use `arrayWeightsQuick()`?
limma
updated 11 days ago by • 0 • written 5 weeks ago by • 0
0
votes
0
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245
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
21 days ago jamiecatalano2 • 0
2
votes
1
reply
458
views
ROAST for small sets
limma mroast
updated 25 days ago by 52k • written 25 days ago by • 0
0
votes
3
replies
2.1k
views
RE:proper pooling design
Microarray Normalization affy makecdfenv limma marray Microarray Normalization affy limma
written 21.3 years ago by ▴ 70
2
votes
2
replies
1.3k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 7 weeks ago by ★ 4.8k • written 7 weeks ago by • 0
2
votes
3
replies
736
views
Explanation for ROAST results
CAMERA limma
updated 7 weeks ago by 52k • written 7 weeks ago by • 0
5
votes
3
replies
884
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 8 weeks ago by 52k • written 8 weeks ago by ▴ 10
2
votes
2
replies
1.2k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
9 weeks ago • updated 8 weeks ago Elizabeth • 0
1
vote
8
replies
2.0k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 6 months ago by • 0
5
votes
5
replies
1.4k
views
Limma with covariates
limma
written 11 months ago by ▴ 20
1
vote
2
replies
878
views
Differential expression of proteins using somascan data
somascan limma
written 10 weeks ago by • 0
2
votes
4
replies
1.1k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
12 weeks ago • updated 10 weeks ago svlachavas ▴ 840
9
votes
6
replies
2.0k
views
Unbalanced experiment with multiple samples from each patient.
limma
updated 11 weeks ago by • 0 • written 7.4 years 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 3 months ago by • 0 • written 3.7 years ago by • 0
1
vote
2
replies
551
views
contrast matrix design for a continuous variable
limma
5 months ago • updated 3 months ago dtzhu337 • 0
3
votes
5
replies
1.5k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 4 months ago by 68k • written 4 months ago by ▴ 10
2
votes
5
replies
554
views
Differential variability modelling with vst() expression
limma DESeq2
written 4 months ago by • 0
0
votes
0
replies
225
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
4 months ago GJ • 0
0
votes
2
replies
522
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 4 months ago by ▴ 840
6
votes
5
replies
799
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 4 months ago by 68k • written 4 months ago by • 0
4
votes
4
replies
873
views
Warning message when running limma with covariates
limma
10 months ago • updated 4 months ago Chris ▴ 20
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 5 months ago by ▴ 30
0
votes
2
replies
594
views
Cross-validation with multiple control subgroups in limma
limma multtest
4 months ago Ali Barry ▴ 40
3
votes
3
replies
823
views
Crossover design with limma
limma crossover
updated 5 months ago by 52k • written 5 months ago by ▴ 30
0
votes
2
replies
456
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
5 months ago Tadeoye ▴ 20
6
votes
10
replies
3.0k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 5 months ago by ★ 4.8k • written 5 months ago by ▴ 10
0
votes
2
replies
648
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 5 months ago by 52k • written 5 months ago by ▴ 10
2
votes
3
replies
1.5k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 5 months ago by 68k • written 5 months ago by ▴ 10
0
votes
9
replies
1.3k
views
Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 5 months ago by 68k • written 5 months ago by • 0
1
vote
3
replies
592
views
Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 5 months ago by • 0
0
votes
5
replies
914
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
6 months ago • updated 5 months ago abadgerw • 0
1
vote
3
replies
619
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
6 months ago • updated 5 months ago abadgerw • 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
0
votes
2
replies
303
views
List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
6 months ago • updated 5 months ago giulia.gentile ▴ 10
4
votes
2
replies
833
views
Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 6 months ago by 52k • written 6 months ago by ▴ 60
1
vote
2
replies
364
views
Limma Interaction Effect with Covariates
limma DMRcate
6 months ago kitzhu • 0
2
votes
3
replies
1.1k
views
[How to construct a model.matrix ]
limma modelmatrix
updated 6 months ago by 52k • written 6 months ago by • 0
8
votes
3
replies
4.6k
views
Appropriate ways to filter counts data for voom/limma
limma edger sequencing
written 8.8 years ago by ▴ 10
3
votes
4
replies
915
views
Limma- Print-tip loess normalisation-printer layout information does not match M row dimension
Normalization limma within-arraynormalisation Printerlayout
6 months ago dseauer • 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
0
votes
1
reply
724
views
Issue with weights in voomLmFit()
limma
updated 6 months ago by 52k • written 19 months ago by ▴ 170
1
vote
2
replies
1.2k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
6 months ago Ai • 0
4
votes
3
replies
998
views
Analysis of 2*4 factorial design
limma
updated 6 months ago by 52k • written 6 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
7 months ago • updated 6 months ago altintas.ali • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Check removeBatchEffect effectiveness by Gordon Smyth 52k
Both of your matrices, `design_batcheffects` and `design_timepoint`, span the intercept term, which will cause a warning about NA coefficie…
Comment: DiffBind - question on the use of filtered or unfiltered input data by sloperun3az • 0
Your essay was beneficial to me, and I found it to be very useful. Thank you for writing it. You give a wealth of knowledge that is not onl…
Comment: compute_fasta_digest does not match Salmon index hash by sloperun3az • 0
The people who are reading your work are not taken into consideration, even though you appear to have a solid understanding of the subject …
Comment: parameters of filterByExpr by Paul Harrison ▴ 110
It might be worth trying limma-voom (or limma-trend) instead of a GLM based method. In our experience these are less prone to this problem.…
Comment: limma::voom vs edgeR::voomLmFit - when to use? by Gordon Smyth 52k
voomLmFit() is in edgeR instead of limma because it needs to call edgeR::glmFit() internally to determine which of the zero observations al…
Votes
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
GAlignments Cigar to GRanges
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