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0
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0
answers
5
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0
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Error in data.frame for limmaCtData function
limma software error data.frame written 5 hours ago by azmir004 • 0
2
votes
2
answers
38
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2
answers
Incorporating subject ID as random effect for repeated measures RNA-Seq analysis
limma rna-seq repeated measures mixed model written 14 hours ago by mikhael.manurung • 0 • updated 9 hours ago by Gordon Smyth ♦ 35k
2
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1
answer
139
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1
answer
How to analyze correctly agilent two-colour microarray data from the ArrayExpress repository with the limma R package
limma arrayexpress agilent microarrays nchannelset written 2 days ago by svlachavas • 610 • updated 2 days ago by Gordon Smyth ♦ 35k
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2
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70
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2
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GSVA & Limma for DE of Gene Sets using NanoString Data
limma gsva limma design matrix nanostring limma contrast matrix written 5 days ago by seblatt • 0 • updated 2 days ago by Robert Castelo • 2.2k
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1
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60
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1
answer
mroast/fry with gene weights for most or all genes
limma mroast fry written 9 days ago by maltethodberg • 100 • updated 3 days ago by Gordon Smyth ♦ 35k
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1
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50
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1
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Limma analysis combining twins pairs and unpaired controls
rnaseq limma twin analysis written 6 days ago by kalletrontti • 0 • updated 5 days ago by Aaron Lun • 21k
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1
answer
44
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1
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Visualization of analysis of multiple cell lines
limma plotmds cell lines written 6 days ago by Alexander Az. • 0 • updated 6 days ago by Gordon Smyth ♦ 35k
2
votes
1
answer
125
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1
answer
Limma: The log2FC of topTable is not equal to Mean(log2CPM) of Basal - Mean(log2CPM) of LP
limma written 8 days ago by zhouqz • 0 • updated 7 days ago by Aaron Lun • 21k
6
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1
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45
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5 follow
1
answer
Pre-ranked camera gene set testing with edgeR results
limma edger camera gene set testing camerapr written 8 days ago by jamie.gearing • 40 • updated 8 days ago by Gordon Smyth ♦ 35k
0
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1
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55
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1
answer
Gene set enrichment analysis with ChIP-seq data using test statistics directly
limma csaw written 8 days ago by gabriel.hoffman • 0 • updated 8 days ago by Aaron Lun • 21k
3
votes
1
answer
153
views
1
answer
limma Multi-level Experiments correcting for continuous covariates
limma methylation limma design matrix covariates epic written 14 days ago by c.bettencourt • 0 • updated 9 days ago by Aaron Lun • 21k
2
votes
1
answer
108
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1
answer
Why my limma DEG result in top Table all without significant meaning,showing logFC <1.5 or logFC>-1.5 ?
limma toptable logfc deg written 11 days ago by Biomed • 0 • updated 10 days ago by Gordon Smyth ♦ 35k
1
vote
1
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59
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1
answer
Identifying correlation between two variables using Limma
limma R written 13 days ago by repinementer • 0 • updated 13 days ago by Gordon Smyth ♦ 35k
5
votes
2
answers
104
views
7 follow
2
answers
Limma example where one comparison gives different results depending on the matrix formulation
limma written 13 days ago by alexgraehl • 20 • updated 13 days ago by Gordon Smyth ♦ 35k
0
votes
1
answer
599
views
1
answer
Use probesets with highest baseline expression for differential gene
annotation probe limma written 6.6 years ago by Gordon Smyth ♦ 35k
1
vote
1
answer
142
views
1
answer
Using Limma to normalize data sets
affy limma written 15 days ago by mahm • 20 • updated 15 days ago by thokall • 120
2
votes
1
answer
87
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1
answer
Creating a correct limma model with respect to contrast matrix and design matrix
limma limma design matrix limma contrast matrix written 16 days ago by payam_delfani1980 • 0 • updated 15 days ago by Aaron Lun • 21k
1
vote
1
answer
103
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1
answer
Is there an equivalent function for write.fit() that produces values/output in R console?
limma write.fit written 18 days ago by payam_delfani1980 • 0 • updated 18 days ago by Gordon Smyth ♦ 35k
0
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2
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579
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2
answers
[maSigPro] two color array analysis of time series in different cell lines.???
limma masigpro written 4.9 years ago by neeraj rana • 60 • updated 19 days ago by sbbinfo90 • 0
2
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1
answer
110
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1
answer
Limma: Differential expression for micro RNA sequence data
limma mirna-seq written 20 days ago by Michael Stone • 0 • updated 20 days ago by Gordon Smyth ♦ 35k
2
votes
2
answers
140
views
2
answers
Get the countsFromAbundance as limma input
limma deseq2 differential expression tximport written 20 days ago by Darklings • 0 • updated 20 days ago by Gordon Smyth ♦ 35k
3
votes
1
answer
65
views
1
answer
DE genes comparison of different treatments from microarray and RNAseq data
microarray limma edger deseq2 written 22 days ago by Bio_Ram • 0 • updated 22 days ago by James W. MacDonald ♦ 47k
1
vote
1
answer
144
views
1
answer
Do the gene set statistics of the ROAST paper correspond to those implemented in the .roastEffects R function?
limma statistics roast source code gene set testing written 27 days ago by Andrea Carenzo • 0
3
votes
1
answer
62
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1
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Can limma/other DE algorithms be used for differential analysis of chemical descriptors?
cheminformatics limma edger deseq2 written 27 days ago by perdedorium • 0 • updated 27 days ago by Aaron Lun • 21k
5
votes
2
answers
98
views
2
answers
Reading and normalizing two-color Agilent microarrays
limma agilent microarrays written 29 days ago by dr • 10 • updated 28 days ago by Peter Langfelder • 1.5k
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