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0
votes
1
answer
75
views
1
answer
Count filter for differential expression
limma edger counts written 1 day ago by kaur • 0 • updated 9 hours ago by Gordon Smyth ♦ 35k
2
votes
1
answer
108
views
1
answer
t-statistic from various limma-approaches does not follow the theoretical distribution
limma voom robust regression voomwithqualityweights t-statistic written 12 days ago by brynedal • 0
0
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1
answer
94
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1
answer
Controlling numerical covariates: differential gene expression with limma voom
rnaseq limma R voom differential gene expression written 6 days ago by Onyi Ukay • 0 • updated 6 days ago by mikhael.manurung • 10
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1
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57
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1
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Setting up the design for paired analysis
limma edger paired design written 7 days ago by candida.vaz • 30 • updated 6 days ago by James W. MacDonald ♦ 48k
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2
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93
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2
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Interpreting mroast results
limma roast mroast written 10 days ago by SB • 0
2
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1
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96
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1
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Inconsistent result between limma/voom and DESeq2
rnaseq limma deseq2 voom limma-voom written 11 days ago by bharata1803 • 20 • updated 11 days ago by Gordon Smyth ♦ 35k
0
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2
answers
90
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2
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RNA-seq analysis using R
rnaseq limma convert R written 12 days ago by justinkablan225 • 0 • updated 11 days ago by Gordon Smyth ♦ 35k
3
votes
1
answer
66
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1
answer
Limma Voom duplicateCorrelation Design
limma duplicatecorrelation voom written 13 days ago by bruce.moran • 20 • updated 13 days ago by Aaron Lun • 21k
5
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2
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166
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2
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edgeR paired samples with blocking
limma edger paired samples blocking written 18 days ago by anou • 0 • updated 14 days ago by Gordon Smyth ♦ 35k
2
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1
answer
97
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1
answer
Using LIMMA for differential gene analysis of microarray data
limma differential gene expression affymetrix microarrays ncbi geo written 4 weeks ago by Francesca McGrath • 0 • updated 4 weeks ago by Aaron Lun • 21k
0
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1
answer
79
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1
answer
Removing redundancy in Reactome pathways after performing gene set analysis with camera
limma camera gene set analysis gene set enrichment written 4 weeks ago by emeline.perthame • 0 • updated 4 weeks ago by Gordon Smyth ♦ 35k
1
vote
1
answer
68
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1
answer
batch effect - Limma package
limma written 4 weeks ago by dressa_ol • 0 • updated 4 weeks ago by James W. MacDonald ♦ 48k
0
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1
answer
91
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1
answer
RNAseq gene expression analysis in Personalized genomics
limma edger deseq2 tcga written 5 weeks ago by bioc.vkas • 0 • updated 5 weeks ago by Michael Love ♦ 20k
0
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1
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106
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1
answer
Creating a design matrix
limma design matrix written 3 months ago by mahm • 20 • updated 5 weeks ago by Gordon Smyth ♦ 35k
0
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2
answers
111
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2
answers
limma and intercept
limma intercept written 5 weeks ago by Nicolas Servant • 230
1
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2
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76
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2
answers
genes repeated in the heatmap several times(10x) when using limma
normalization cancer limma design and contrast matrix heatmap written 6 weeks ago by andreilazar9 • 0 • updated 6 weeks ago by Axel Klenk • 920
3
votes
2
answers
81
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2
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Is it ok to use decideTests on linearly dependent contrasts?
limma decidetests written 6 weeks ago by Ryan C. Thompson ♦ 7.0k • updated 6 weeks ago by Gordon Smyth ♦ 35k
0
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1
answer
137
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1
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Limma Design Matrix for Paired Samples with Confouding Factors
limma design matrix paired samples confounding factors written 6 weeks ago by yuabrahamliu • 0 • updated 6 weeks ago by Aaron Lun • 21k
0
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1
answer
121
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1
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Any difference between v$E and cpm(keep,log=TRUE)
limma written 7 weeks ago by Raymond • 0 • updated 7 weeks ago by Gordon Smyth ♦ 35k
2
votes
2
answers
112
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2
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Queries related to limma package based analysis of masspectrometry data
limma written 7 weeks ago by manubhaikp • 10 • updated 7 weeks ago by Gordon Smyth ♦ 35k
4
votes
1
answer
94
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1
answer
limma barcodeplot(): calculation of enrichment score
limma gene set enrichment analysis written 7 weeks ago by khandarius • 20 • updated 7 weeks ago by Aaron Lun • 21k
1
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1
answer
95
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1
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Differential Expression of GSVA Enrichment Scores - pre-processing with voomWithQualityWeights and GSVA follow-up with lmfit
limma gsva lmfit voomwithqualityweights written 7 weeks ago by SB • 0 • updated 7 weeks ago by Robert Castelo • 2.2k
1
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1
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130
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1
answer
Explanation of mroast results for specific biological processes and error with barcodeplot function with a microarray dataset
limma mroast barcodeplot agilent microarrays go.bp written 8 weeks ago by svlachavas • 610 • updated 8 weeks ago by Gordon Smyth ♦ 35k
0
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2
answers
170
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2
answers
Limma Volcano Plot Highlight Top Genes by Color
microarray limma volcanoplot color written 8 weeks ago by dmm204 • 0 • updated 8 weeks ago by Gordon Smyth ♦ 35k
0
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0
answers
56
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0
answers
Sva for tumor cellular heterogeneity
limma sva written 8 weeks ago by chp950 • 0
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