Showing : Limma • reset
0
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RE:proper pooling design
Microarray Normalization affy makecdfenv limma marray Microarray Normalization affy limma
updated 6 days ago by • 0 • written 21.3 years ago by ▴ 70
0
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2
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444
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
updated 7 days ago by 52k • written 12 days ago by ▴ 10
2
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3
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1.3k
views
how to use `arrayWeightsQuick()`?
limma
updated 9 days ago by 52k • written 11 days ago by • 0
2
votes
2
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1.2k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 25 days ago by ★ 4.8k • written 26 days ago by • 0
2
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3
replies
680
views
Explanation for ROAST results
CAMERA limma
updated 25 days ago by 52k • written 26 days ago by • 0
5
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3
replies
825
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Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 4 weeks ago by 52k • written 4 weeks ago by ▴ 10
2
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2
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1.1k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
5 weeks ago • updated 4 weeks ago Elizabeth • 0
1
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8
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1.8k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 5 months ago by • 0
5
votes
5
replies
1.2k
views
Limma with covariates
limma
written 10 months ago by ▴ 20
1
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2
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831
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Differential expression of proteins using somascan data
somascan limma
written 6 weeks ago by • 0
2
votes
4
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965
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
8 weeks ago • updated 6 weeks ago svlachavas ▴ 840
8
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6
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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
0
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3
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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 9 weeks ago by • 0 • written 3.7 years ago by • 0
1
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2
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524
views
contrast matrix design for a continuous variable
limma
4 months ago • updated 3 months ago dtzhu337 • 0
3
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5
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1.4k
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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
2
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5
replies
504
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Differential variability modelling with vst() expression
limma DESeq2
written 3 months ago by • 0
0
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0
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199
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Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
3 months ago GJ • 0
0
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2
replies
493
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 3 months ago by ▴ 840
6
votes
5
replies
751
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
4
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4
replies
837
views
Warning message when running limma with covariates
limma
10 months ago • updated 3 months ago Chris ▴ 20
1
vote
9
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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
2
replies
567
views
Cross-validation with multiple control subgroups in limma
limma multtest
4 months ago • updated 3 months ago Ali Barry ▴ 40
3
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3
replies
785
views
Crossover design with limma
limma crossover
updated 4 months ago by 52k • written 4 months ago by ▴ 30
0
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2
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428
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Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
4 months ago Tadeoye ▴ 20
6
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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
0
votes
2
replies
610
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 4 months ago by 52k • written 4 months ago by ▴ 10
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
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
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3
replies
565
views
Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 4 months ago by • 0
0
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5
replies
872
views
Merge Replicates vs Mixed Model
limma DifferentialExpression variancePartition dream
5 months ago • updated 4 months ago abadgerw • 0
1
vote
3
replies
590
views
makeContrastsDream for Interaction
limma DifferentialExpression variancePartition dream
5 months ago • updated 4 months ago abadgerw • 0
2
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12
replies
2.2k
views
limma technical repeat correction
limma lmer duplicateCorrelation technicalrepeats
5 months ago • updated 4 months ago john • 0
0
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2
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290
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List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
5 months ago giulia.gentile ▴ 10
4
votes
2
replies
752
views
Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 5 months ago by 52k • written 5 months ago by ▴ 60
1
vote
2
replies
340
views
Limma Interaction Effect with Covariates
limma DMRcate
5 months ago kitzhu • 0
2
votes
3
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1.1k
views
[How to construct a model.matrix ]
limma modelmatrix
updated 5 months ago by 52k • written 5 months ago by • 0
8
votes
3
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4.5k
views
Appropriate ways to filter counts data for voom/limma
limma edger sequencing
written 8.7 years ago by ▴ 10
3
votes
4
replies
881
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
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
0
votes
1
reply
712
views
Issue with weights in voomLmFit()
limma
updated 5 months ago by 52k • written 18 months ago by ▴ 170
1
vote
2
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1.1k
views
Consistent Decimals In Data After Antibody Array Background Correction Using Limma:nec Function
limma MicroarrayData Normalization
5 months ago Ai • 0
4
votes
3
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964
views
Analysis of 2*4 factorial design
limma
updated 5 months ago by 52k • written 5 months ago by • 0
4
votes
6
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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
3
votes
2
replies
2.1k
views
Multi-level design RRBS analysis with voomLmFit
edgeR voomLmFit limma duplicateCorrelation voom
updated 5 months ago by 52k • written 3.4 years 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
4
votes
6
replies
1.7k
views
LIMMA Differing P-Values for Treatment-Contrast Parameterization vs Group-Means Parameterization
limma
updated 5 months ago by 52k • written 6 months ago by • 0
0
votes
3
replies
556
views
Need help interpreting heatmaps from limma
limma
written 6 months ago by • 0
2
votes
2
replies
562
views
Automatically generate contrasts from a model matrix / formula
limma
updated 6 months ago by ★ 4.8k • written 6 months ago by ▴ 10
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
3
votes
3
replies
469
views
How to subset voomLmFit (MArrayLM) object?
limma edgeR
6 months ago Guido Hooiveld ★ 4.1k
50 results • Page 1 of 1
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Comment: DeSeq Strategies for run to run Replication by Michael Love 43k
You shouldn't need to run `DESeq` on the test data, or manually compute normalization factors. ``` dds_test <- ... # create object dds_te…
Answer: Feature Counts - potential bug with outfile.jcounts by Wei Shi ★ 3.6k
We have made significant changes to how featureCounts annotates junctions detected in read mapping results. These updates are included in t…
Comment: How to perform batch correction on scRNA-seq with confounding plate effects? by 瑞宏 • 0
I would like to share my own understanding: in single-cell RNA sequencing (scRNA-seq), batch correction is solely intended to identify the …
Comment: DiffBind can't find a DAR by Mengjun • 0
Additionally, i checked my bigwig in igv, it shows that the ctrl_1 is more like ko_1, and ctrl_2's track is more like ko_2's track. Did an…
Comment: European Bioconductor Conference 2023 planning by ht • 0
Great news about the European Bioconductor Conference 2023 planning! As someone who enjoys statistical computing and bioinformatics, I'm ex…
Votes
Comment: Differential expression analysis using two TCGA datasets
C: Annotating HTA 2.0 genes
C: Annotating HTA 2.0 genes
A: Annotating HTA 2.0 genes
A: Annotating HTA 2.0 genes
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