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0
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1
answer
25
views
1
answer
how to apply correctly geneSetTest on deseq2 data results
limma deseq2 written 9 hours ago by jarod_v6@libero.it • 20 • updated 9 hours ago by Michael Love ♦ 12k
7
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2
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2
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limma: same data in different formats produces different DEG-analysis results
limma written 3 days ago by littlefishes20 • 10
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3
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58
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3
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Identification of DEGs through limma analysis
microarray limma p values lfc degs written 1 day ago by rkp • 0 • updated 22 hours ago by Gordon Smyth ♦ 30k
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1
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72
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1
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limma regularization on Ballgown
limma ballgown written 21 days ago by rodri2006 • 0 • updated 7 days ago by Alyssa Frazee • 110
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1
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45
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1
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How to extract DEG using limma at threshold value p<0.05 and fold change >1.5 ?
microarray limma R bioconductor written 8 days ago by rkp • 0 • updated 8 days ago by Aaron Lun • 15k
4
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1
answer
66
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1
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Limma is doing the right way to calculate the fold change?
proteomics limma written 10 days ago by Bioinformatics • 20 • updated 10 days ago by Laurent Gatto ♦ 810
2
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1
answer
63
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1
answer
Correcting for Batch Effects Prior to Differential Gene Expression Analysis with limma
limma rna-seq batch effect written 13 days ago by adscheid3 • 0 • updated 13 days ago by Aaron Lun • 15k
2
votes
2
answers
90
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2
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Trouble with DESeq2, edgeR, and limma not accepting zeros in input
limma edger deseq2 written 13 days ago by Kaustav • 0 • updated 13 days ago by Gordon Smyth ♦ 30k
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1
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54
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1
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LIMMA 2x2 with time
limma limma design matrix written 14 days ago by Ahdee • 30 • updated 13 days ago by James W. MacDonald ♦ 43k
1
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1
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91
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1
answer
unable to update packages: foreign, Matrix
limma design and contrast matrix written 14 days ago by Bioinformatics • 20 • updated 14 days ago by James W. MacDonald ♦ 43k
6
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1
answer
88
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1
answer
differential expression analysis of htseq data with edgeR/voom
limma edger voom htseq rnaseq123 written 14 days ago by wd • 10 • updated 14 days ago by Aaron Lun • 15k
0
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1
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1
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Limma - RNA-Seq DE genes - Quantile normalized log transformed RPKM data
limma written 5.6 years ago by Avinash S • 40 • updated 15 days ago by Gordon Smyth ♦ 30k
2
votes
1
answer
83
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1
answer
Limma Model Design
microarray limma methylation written 17 days ago by Sarah Nesbitt • 0 • updated 17 days ago by Aaron Lun • 15k
2
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1
answer
81
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1
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Limma toptable interpretation check
microarray limma fdr results p-value written 23 days ago by bhgyu • 0 • updated 23 days ago by Aaron Lun • 15k
0
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0
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64
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0
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queries reg hub genes
microarray annotation normalization limma written 26 days ago by krithi11987 • 0
4
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2
answers
137
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2
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Alternative packages to limma for analysis of microarray datasets
microarray limma deg written 5 weeks ago by Maximilian • 10 • updated 4 weeks ago by Bernd Klaus • 430
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1
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82
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1
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bug limma / illuminaio? Otherwise small feature request...
limma illuminaio idat gzip written 4 weeks ago by Guido Hooiveld • 2.1k • updated 4 weeks ago by Matthew Ritchie • 630
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61
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prior.prob has opposite effects in goana and kegga?
limma goana kegga missmethyl gometh written 5 weeks ago by Jenny Drnevich • 1.8k
3
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2
answers
105
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2
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limma for Paired Samples vs. lme
limma linear model paired samples written 5 weeks ago by wewolski • 10 • updated 5 weeks ago by Aaron Lun • 15k
2
votes
1
answer
90
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1
answer
Limma filtering based on treatment group
limma filtering written 5 weeks ago by jamie.gearing • 0 • updated 5 weeks ago by Steve Lianoglou ♦ 12k
0
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4
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247
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4
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Is anyone able to explain the statistics behind the dmpFinder function in minfi package?
limma minfi methylation dmpfinder written 9 months ago by mcall • 0 • updated 5 weeks ago by vulegom • 0
0
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1
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100
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1
answer
read.maimages(targets, source="genepix") Error in `[.data.frame`(obj, , columns[[a]]) : undefined columns selected
limma bioconductor agilent microarrays written 5 weeks ago by sankhwar.madhu • 0 • updated 5 weeks ago by James W. MacDonald ♦ 43k
12
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1
answer
169
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1
answer
Testing for DE genes
limma differential gene expression affymetrix microarrays written 5 weeks ago by Lennart.Vermander • 10 • updated 5 weeks ago by Aaron Lun • 15k
0
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0
answers
103
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0
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Agilent data normalization
limma written 5 weeks ago by mona.salehinasab • 0
2
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1
answer
115
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1
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Limma: difference between groups of paired data
limma limma paired analysis written 6 weeks ago by johnmcma • 0 • updated 6 weeks ago by Aaron Lun • 15k
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