Showing : LIMMA • reset
4
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2
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294
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When to use edgeR or limma
edgeR limma
updated 12 days ago by 53k • written 15 days ago by • 0
0
votes
2
replies
302
views
Combining two proteomics datasets with limpa
limpa ProteomicsWorkflow limma
21 days ago • updated 7 days ago Andrew Pattison • 0
4
votes
2
replies
440
views
Limma-voom sample weights and impact on DEG numbers
limma
5 weeks ago • updated 24 days ago A.Barden ▴ 20
0
votes
4
replies
621
views
How does contrasts.fit do in limma to extract comparisons with a model having interaction terms?
limma
updated 23 days ago by • 0 • written 5 weeks ago by • 0
0
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1
reply
1.3k
views
two questions about limma
Microarray limma Microarray limma
updated 8 weeks ago by 53k • written 18.9 years ago by ▴ 240
2
votes
2
replies
319
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Identifying differentially expressed genes in individual samples from a large cohort
limma DifferentialExpression
10 weeks ago jamie.gearing ▴ 60
1
vote
2
replies
410
views
Can limma be used with module eigengenes instead of genes?
limma WGCNA GSVA
written 5 months ago by ▴ 20
0
votes
1
reply
260
views
How to model DE for RNA-seq in concordant monozygotic twins?
RNASeq variancePartition RUVSeq limma edgeR
updated 3 months ago by 53k • written 3 months ago by • 0
5
votes
13
replies
1.5k
views
Guidance on limma for pseudobulk scRNA-seq with multi-factor design
limma RNASeq scRNAseq
updated 4 months ago by 53k • written 4 months ago by • 0
0
votes
4
replies
492
views
voomLmFit fitted log-CPM values
limma edgeR
updated 4 months ago by 53k • written 4 months ago by ▴ 10
1
vote
3
replies
416
views
ROAST compare results with complex design
limma mroast roast CAMERA
written 4 months ago by • 0
2
votes
8
replies
809
views
Are voomByGroup and voomLmFit compatible?
limma voomLmFit voomByGroup
updated 4 months ago by 53k • written 5 months ago by ▴ 30
3
votes
4
replies
633
views
p-adjusted values in multiple comparisons
StatisticalMethod limma RnaSeqSampleSizeData
updated 4 months ago by • 0 • written 5 months ago by • 0
1
vote
2
replies
429
views
Difference between logFC in limma-voom and weighted limma-voom
limma voom weighting
5 months ago richardallenfriedmanbrooklyn ▴ 30
3
votes
1
reply
482
views
Limpa Pipeline Order
limma limpa
updated 5 months ago by 53k • written 5 months ago by • 0
3
votes
2
replies
495
views
Should voomWithQualityWeights still be used when the sample-specific weights vary between the groups of interest?
limma
updated 5 months ago by 53k • written 5 months ago by ▴ 20
0
votes
8
replies
712
views
How to use limma to analyze complex temporal RNAseq data
timecourse RNASeq limma
5 months ago Jiahao Tian • 0
2
votes
2
replies
479
views
Limma : paired samples leading to unexpected estimates
limma
6 months ago Basti ▴ 780
2
votes
2
replies
609
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
2.0k
views
Should Xenium pseudobulk experiments be analysed like microarrays (limma) or like RNASeq (edgeR,Deseq2, or limma-voom)
Deseq2 edgeR limma xenium Voom
6 months ago richardallenfriedmanbrooklyn ▴ 30
7
votes
9
replies
5.8k
views
competitive enrichment test yields too few significant results, self-contained too many
limma DESeq2 fry edgeR
6 months ago bbao ▴ 10
0
votes
1
reply
1.5k
views
How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
Microarray limma BRAIN Microarray limma BRAIN
updated 6 months ago by 53k • written 17.0 years ago by ▴ 10
0
votes
3
replies
2.5k
views
Applying lmFit(), eBayes() and topTable() for modeling associations between NMR-derived metabolic measures and various traits
limma Bioconductor Metabolomics
updated 6 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
7 months ago Eric • 0
3
votes
2
replies
6.4k
views
limma duplicateCorrelation appropriate where some blocks cross condition and some are in same condition?
limma
8 months ago Geoff • 0
2
votes
3
replies
1.6k
views
Differential gene expression analysis on haplotype-resolved diploid assembly
edgeR DESeq2 haplotype limma
8 months ago Paulito • 0
0
votes
1
reply
521
views
Typo in the help of lmFit()
limma
updated 8 months ago by 53k • written 8 months ago by • 0
0
votes
2
replies
728
views
Limma suqeezeVar
limma
8 months ago Mengchun • 0
0
votes
2
replies
1.5k
views
Limma trend with limpa
limpa limma trend
updated 8 months ago by 53k • written 8 months ago by • 0
2
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5
replies
1.4k
views
Dealing with heteroscedascity in limma
limma splines Proteomics
written 8 months ago by • 0
5
votes
7
replies
3.5k
views
limma correction for tumor purity
limma
8 months ago gabriella.jacobson-eisenberg ▴ 20
0
votes
3
replies
1.1k
views
Model performance for spline modelling of RNA-seq timecourses in edgeR
edgeR limma
written 9 months ago by ▴ 10
4
votes
7
replies
3.5k
views
Check removeBatchEffect effectiveness
RNAseq limma removeBatchEffect
9 months ago • updated 3 months ago massimo ▴ 10
0
votes
0
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512
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
768
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 8 months ago by • 0 • written 9 months ago by • 0
2
votes
2
replies
1.6k
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
1.3k
views
Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with multiple cell types
edgeR limma voomLmFit
updated 10 months ago by 53k • written 10 months ago by ▴ 10
2
votes
2
replies
1.7k
views
Limma - Complex 2-way multi-level contrast with paired samples
edgeR contrastmatrix limma
10 months ago Elizabeth • 0
1
vote
2
replies
1.2k
views
Differential expression of proteins using somascan data
somascan limma
written 10 months ago by • 0
2
votes
4
replies
1.7k
views
Use of limma R package with targeted proteomics for DE analysis
DEanalysis limma olinktargetedproteomics
11 months ago svlachavas ▴ 840
3
votes
5
replies
2.4k
views
Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
limma edgeR biomaRt
updated 12 months ago by 68k • written 12 months ago by ▴ 10
0
votes
0
replies
418
views
Testing Differential Expression with Interaction Effect Between Categorical and Continuous Variable with Repeated (Paired) Measures using variancePar…
limma variancePartition
12 months ago GJ • 0
0
votes
2
replies
733
views
Paired analysis in proteomics data for DE while interested in only a particular subset of the data
limma modelmatrix pairedanalysis Proteomics
written 12 months ago by ▴ 840
2
votes
5
replies
977
views
Differential variability modelling with vst() expression
limma DESeq2
written 12 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 12 months ago by 68k • written 13 months ago by • 0
0
votes
2
replies
864
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 13 months ago by ▴ 40
0
votes
2
replies
789
views
Advice needed: Using limma for differential pathway analysis with continuous disease progression scores
limma DifferentialExpression Designmatrix
13 months ago Tadeoye ▴ 20
4,230 results • Page 1 of 85
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Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by varying.mastodon.isyn • 0
Oh, that error! I remember wrestling with that one for hours when I was first learning Python. Turns out I was trying to use a list itself …
Comment: Confirm that OpenStats will not be archived (pryr dependency) by Marina • 0
Thank you!
Comment: AnnotationForge makeOrgPackage rsqlite_send_query error by ansley.r.burtch • 0
Hi! I am sure you are well into your career now and haven't worked on this for a while, but I wanted to let you know this is still helping …
Comment: limpa analysis advice by Gordon Smyth 53k
I prefer for limpa to work on precursor intensities, because my understanding is that precursors are the basic unit of identification and q…
Answer: Confirm that OpenStats will not be archived (pryr dependency) by shepherl 4.3k
As long as OpenStats is building cleanly and all needed stated dependencies are on CRAN or Bioconductor, OpenStats will not be archived. I…
Votes
Comment: Normalise to a housekeeping gene in DESEq2
Comment: limpa analysis advice
C: AnnotationForge makeOrgPackage rsqlite_send_query error
Answer: Limpa Pipeline Order
Answer: Array weights in dpcDE
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