Showing : Limma • reset
1
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4
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239
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Bulk RNAseq analysis for
DESeq2 RNASeq edgeR limma
3 days ago • updated 2 days ago Mariami • 0
4
votes
2
replies
400
views
When to use edgeR or limma
edgeR limma
updated 27 days ago by 53k • written 29 days ago by • 0
0
votes
2
replies
383
views
Combining two proteomics datasets with limpa
limpa ProteomicsWorkflow limma
5 weeks ago • updated 22 days ago Andrew Pattison • 0
5
votes
3
replies
639
views
Limma-voom sample weights and impact on DEG numbers
limma
written 7 weeks ago by ▴ 20
0
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4
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659
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How does contrasts.fit do in limma to extract comparisons with a model having interaction terms?
limma
updated 5 weeks ago by • 0 • written 8 weeks ago by • 0
2
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2
replies
347
views
Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
12 weeks ago jamie.gearing ▴ 60
0
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1
reply
281
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 4 months ago by 53k • written 4 months ago by • 0
5
votes
13
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1.6k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 4 months ago by 53k • written 5 months ago by • 0
0
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4
replies
509
views
voomLmFit fitted log-CPM values
limma edgeR
updated 5 months ago by 53k • written 5 months ago by ▴ 10
1
vote
3
replies
437
views
ROAST compare results with complex design
limma mroast roast CAMERA
written 5 months ago by • 0
3
votes
4
replies
664
views
p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 4 months ago by • 0 • written 6 months ago by • 0
2
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8
replies
840
views
Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 5 months ago by 53k • written 6 months ago by ▴ 30
1
vote
2
replies
424
views
Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 6 months ago by ▴ 20
1
vote
2
replies
448
views
Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
6 months ago richardallenfriedmanbrooklyn ▴ 30
3
votes
1
reply
528
views
Limpa Pipeline Order
limma limpa
updated 6 months ago by 53k • written 6 months ago by • 0
3
votes
2
replies
508
views
Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 6 months ago by 53k • written 6 months ago by ▴ 20
0
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8
replies
740
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
6 months ago Jiahao Tian • 0
2
votes
2
replies
501
views
Limma : paired samples leading to unexpected estimates
limma
6 months ago Basti ▴ 780
2
votes
2
replies
649
views
(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
6 months ago sandmann.t ▴ 70
4
votes
8
replies
2.1k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
7 months ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
replies
5.9k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
7 months ago bbao ▴ 10
0
votes
3
replies
2.6k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma Bioconductor Metabolomics
updated 7 months ago by 53k • written 7 months ago by • 0
0
votes
4
replies
1.9k
views
How to use goana function with zebrafish genome from org.Dr.eg.db
org.Dr.eg.db zebrafish limma
8 months ago Eric • 0
3
votes
2
replies
6.5k
views
limma duplicateCorrelation appropriate where some blocks cross condition and some are in same condition?
limma
8 months ago Geoff • 0
2
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3
replies
1.7k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
8 months ago Paulito • 0
0
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1
reply
531
views
Typo in the help of lmFit()
limma
updated 8 months ago by 53k • written 8 months ago by • 0
0
votes
2
replies
1.6k
views
Limma trend with limpa
limpa limma trend
updated 8 months ago by 53k • written 8 months ago by • 0
0
votes
2
replies
748
views
Limma suqeezeVar
limma
8 months ago Mengchun • 0
2
votes
5
replies
1.4k
views
Dealing with heteroscedascity in limma
limma splines Proteomics
written 9 months ago by • 0
5
votes
7
replies
3.6k
views
limma correction for tumor purity
limma
9 months ago gabriella.jacobson-eisenberg ▴ 20
4
votes
7
replies
3.6k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
9 months ago • updated 4 months ago massimo ▴ 10
0
votes
0
replies
533
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
9 months ago jamiecatalano2 • 0
2
votes
1
reply
792
views
ROAST for small sets
limma mroast
updated 9 months ago by 53k • written 9 months ago by • 0
2
votes
4
replies
2.0k
views
how to use `arrayWeightsQuick()`?
limma
updated 9 months ago by • 0 • written 10 months ago by • 0
0
votes
3
replies
1.2k
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 10 months ago by ▴ 10
2
votes
2
replies
1.7k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 10 months ago by ★ 5.0k • written 10 months ago by • 0
2
votes
4
replies
1.1k
views
Explanation for ROAST results
CAMERA limma
written 10 months ago by • 0
5
votes
3
replies
1.4k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 11 months ago by 53k • written 11 months ago by ▴ 10
2
votes
2
replies
1.8k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
11 months ago Elizabeth • 0
1
vote
2
replies
1.3k
views
Differential expression of proteins using somascan data
somascan limma
written 11 months ago by • 0
2
votes
4
replies
1.8k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
11 months ago svlachavas ▴ 840
3
votes
5
replies
2.5k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 13 months ago by 68k • written 13 months ago by ▴ 10
0
votes
0
replies
438
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
13 months ago GJ • 0
0
votes
2
replies
759
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 13 months ago by ▴ 840
2
votes
5
replies
1.0k
views
Differential variability modelling with vst() expression
limma DESeq2
written 13 months ago by • 0
6
votes
5
replies
1.2k
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 13 months ago by 68k • written 13 months ago by • 0
0
votes
2
replies
887
views
Cross-validation with multiple control subgroups in limma
limma multtest
13 months ago Ali Barry ▴ 40
1
vote
9
replies
1.7k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 14 months ago by ▴ 40
0
votes
2
replies
812
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
14 months ago Tadeoye ▴ 20
0
votes
2
replies
1.0k
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 14 months ago by 53k • written 14 months ago by ▴ 10
4,231 results • Page 1 of 85
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Replies
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2 by colinmccornack • 0
FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Erik Wright ▴ 150
This has to do with the fact that some taxonomies reuse names at the same rank level. Common examples in the SILVA taxonomy are "Incertae S…
Comment: Deseq2 DE analysis of host-pathogen samples (model separately or jointly?) by a2a2ddrhaa • 0
For those taking a break from the lab, the CT777 Game download https://ct7777.pk/ offers a high-performance entry into online mobile gaming…
Answer: Subsetting data verses contrasts [DESeq2]? by ATpoint ★ 5.0k
This has been asked many times before, please search for relevant posts. In short: Generally it is least tedious to not split the data and …
Votes
Answer: Can you colour dendrogram branch clusters in pheatmap?
Comment: Are transformed values from rlog /vst log2 normalized counts?
Are transformed values from rlog /vst log2 normalized counts?
Answer: Bulk RNAseq analysis for
Answer: DiffBind differential analysis
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