Showing : LIMMA • reset
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How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 13 days ago by 53k • written 18 days ago by • 0
5
votes
13
replies
1.0k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 26 days ago by 53k • written 5 weeks ago by • 0
0
votes
4
replies
313
views
voomLmFit fitted log-CPM values
limma edgeR
updated 6 weeks ago by 53k • written 6 weeks ago by ▴ 10
1
vote
3
replies
286
views
ROAST compare results with complex design
limma mroast roast CAMERA
written 6 weeks ago by • 0
2
votes
8
replies
564
views
Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 6 weeks ago by 53k • written 9 weeks ago by ▴ 30
3
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4
replies
375
views
p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 4 weeks ago by • 0 • written 9 weeks ago by • 0
1
vote
1
reply
175
views
Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
updated 9 weeks ago by 53k • written 9 weeks ago by ▴ 10
1
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2
replies
269
views
Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
10 weeks ago richardallenfriedmanbrooklyn ▴ 30
3
votes
1
reply
287
views
Limpa Pipeline Order
limma limpa
updated 10 weeks ago by 53k • written 10 weeks ago by • 0
2
votes
2
replies
342
views
Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 10 weeks ago by 53k • written 10 weeks ago by ▴ 10
0
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8
replies
553
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How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
10 weeks ago Jiahao Tian • 0
2
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2
replies
335
views
Limma : paired samples leading to unexpected estimates
limma
11 weeks ago Basti ▴ 780
2
votes
2
replies
328
views
(Why) do limma's confidence intervals depend on topTable's p.value argument?
limma
11 weeks ago sandmann.t ▴ 70
4
votes
8
replies
1.8k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
3 months ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
replies
5.5k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
3 months ago bbao ▴ 10
0
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1
reply
1.3k
views
How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray limma BRAIN Microarray limma BRAIN
updated 3 months ago by 53k • written 16.7 years ago by ▴ 10
0
votes
3
replies
2.2k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma Bioconductor Metabolomics
updated 3 months ago by 53k • written 3 months ago by • 0
0
votes
4
replies
1.7k
views
How to use goana function with zebrafish genome from org.Dr.eg.db
org.Dr.eg.db zebrafish limma
4 months ago Eric • 0
3
votes
2
replies
6.3k
views
limma duplicateCorrelation appropriate where some blocks cross condition and some are in same condition?
limma
4 months ago Geoff • 0
2
votes
3
replies
1.3k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
5 months ago • updated 4 months ago Paulito • 0
0
votes
1
reply
446
views
Typo in the help of lmFit()
limma
updated 5 months ago by 53k • written 5 months ago by • 0
0
votes
2
replies
631
views
Limma suqeezeVar
limma
5 months ago Mengchun • 0
0
votes
2
replies
632
views
Limma trend with limpa
limpa limma trend
updated 4 months ago by 53k • written 5 months ago by • 0
2
votes
5
replies
1.1k
views
Dealing with heteroscedascity in limma
limma splines Proteomics
written 5 months ago by • 0
5
votes
7
replies
3.3k
views
limma correction for tumor purity
limma
5 months ago gabriella.jacobson-eisenberg ▴ 20
0
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3
replies
921
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 6 months ago by ▴ 10
4
votes
7
replies
3.1k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
5 months ago • updated 12 days ago massimo ▴ 10
0
votes
0
replies
414
views
Significant Probes and Genes differ in Probe and Region level Differential Methylation Analyses
limma probe DMRcate GenomicRanges DifferentialMethylation
5 months ago jamiecatalano2 • 0
2
votes
1
reply
652
views
ROAST for small sets
limma mroast
updated 6 months ago by 53k • written 6 months ago by • 0
2
votes
4
replies
1.8k
views
how to use `arrayWeightsQuick()`?
limma
updated 5 months ago by • 0 • written 6 months ago by • 0
2
votes
2
replies
1.4k
views
Improving performance of edgeR and limma while adjusting for multiple confounders
edgeR limma
updated 6 months ago by ★ 5.0k • written 6 months ago by • 0
2
votes
4
replies
933
views
Explanation for ROAST results
CAMERA limma
written 6 months ago by • 0
5
votes
3
replies
1.1k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 7 months ago by 53k • written 7 months ago by ▴ 10
2
votes
2
replies
1.5k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
7 months ago Elizabeth • 0
1
vote
2
replies
1.0k
views
Differential expression of proteins using somascan data
somascan limma
written 7 months ago by • 0
2
votes
4
replies
1.4k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
8 months ago • updated 7 months ago svlachavas ▴ 840
3
votes
5
replies
1.9k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 9 months ago by 68k • written 9 months ago by ▴ 10
0
votes
0
replies
352
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
9 months ago GJ • 0
0
votes
2
replies
632
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 9 months ago by ▴ 840
2
votes
5
replies
750
views
Differential variability modelling with vst() expression
limma DESeq2
written 9 months ago by • 0
6
votes
5
replies
1.0k
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 9 months ago by 68k • written 9 months ago by • 0
0
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2
replies
744
views
Cross-validation with multiple control subgroups in limma
limma multtest
10 months ago Ali Barry ▴ 40
1
vote
9
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1.4k
views
Normalizing batch effects using technical replicates for DGE analysis between two conditions from 2 different runs
limma DESeq2 edgeR
written 10 months ago by ▴ 40
0
votes
2
replies
655
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
10 months ago Tadeoye ▴ 20
0
votes
2
replies
851
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 10 months ago by 53k • written 10 months ago by ▴ 10
2
votes
3
replies
1.6k
views
How to annotate a limma Elist raw class object with an annotation file
limma AnnotationDbi
updated 10 months ago by 68k • written 10 months ago by ▴ 10
1
vote
2
replies
680
views
contrast matrix design for a continuous variable
limma
10 months ago • updated 9 months ago dtzhu337 • 0
3
votes
3
replies
976
views
Crossover design with limma
limma crossover
updated 10 months ago by 53k • written 10 months ago by ▴ 30
0
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9
replies
1.6k
views
Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 10 months ago by 68k • written 10 months ago by • 0
6
votes
10
replies
3.3k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 10 months ago by ★ 5.0k • written 10 months ago by ▴ 10
4,225 results • Page 1 of 85
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Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G by dzv20413 • 0
Wow, GBCC 2025 sounds amazing, can not wait to see the logo contest results! Also, I just played [Level Devil][1] and it is super addictive…
Comment: Memory error while running alignments by Erik Wright ▴ 150
How much memory is available on the computer? A distance matrix of 50k sequences requires at least 50k*50k/2 * 8 bytes = 10GB, assuming the…
Comment: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by Gabriel • 0
Thank you very much for the reply. However, none of these three options seems to fit: 1) The genes for which NA appears do not have all 0 …
Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by ubjw24 • 0
Thank you for your replies. I got the problem solved by installing mutSignature with this line: ``` devtools::install_github("dami82/mutS…
Comment: DESeq2 design for haplotype MPRA by Rita • 0
Thank you very much, I appreciate it!
Votes
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
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