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0
votes
1
answer
41
views
1
answer
Differential Expression of GSVA Enrichment Scores - pre-processing with voomWithQualityWeights and GSVA follow-up with lmfit
limma gsva lmfit voomwithqualityweights written 1 day ago by seblatt • 0 • updated 1 day ago by Robert Castelo • 2.2k
1
vote
1
answer
58
views
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 3 days ago by svlachavas • 610 • updated 2 days ago by Gordon Smyth ♦ 35k
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2
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83
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2
answers
Limma Volcano Plot Highlight Top Genes by Color
microarray limma volcanoplot color written 5 days ago by dmm204 • 0 • updated 4 days ago by Gordon Smyth ♦ 35k
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0
answers
27
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0
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Sva for tumor cellular heterogeneity
limma sva written 5 days ago by chp950 • 0
3
votes
1
answer
59
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1
answer
How to calculate average log2 CPM with batch effect?
limma edger cpm written 7 days ago by b.nota • 300 • updated 6 days ago by Aaron Lun • 21k
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1
answer
52
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1
answer
makeTxDbFromGFF errors too many NAs and make.splicings
limma maketxdbfromgff written 16 days ago by Karl Lundén • 20 • updated 7 days ago by Hervé Pagès ♦♦ 13k
1
vote
1
answer
99
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1
answer
Perform limma based gene-set testing for a two-group comparison in a microarray dataset regarding specific biological processes
limma mroast gene set testing agilent microarrays fry gene tests written 8 days ago by svlachavas • 610 • updated 7 days ago by Gordon Smyth ♦ 35k
3
votes
1
answer
47
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1
answer
Limma without eBayes, is it indistunguishable from Ordinary Least Square?
bayesian limma ebayes ls written 7 days ago by CantExitVIM • 10 • updated 7 days ago by Gordon Smyth ♦ 35k
3
votes
1
answer
74
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1
answer
Limma: Don't have .CEL Affymatrix Files.
limma affymetrix written 11 days ago by CantExitVIM • 10 • updated 11 days ago by Gordon Smyth ♦ 35k
0
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0
answers
30
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0
answers
Creating qPCRset object from Bio-Rad CFX file
limma htqpcr written 12 days ago by dbars • 0
5
votes
1
answer
102
views
1
answer
nestedF in decideTests: an analogue of Anova with post-hoc t-tests?
limma anova decidetests written 19 days ago by mikhael.manurung • 10 • updated 17 days ago by Gordon Smyth ♦ 35k
5
votes
1
answer
79
views
1
answer
How barcode-plot enrichment is calculated?
limma camera barcodeplot written 19 days ago by elim • 0 • updated 19 days ago by Gordon Smyth ♦ 35k
5
votes
1
answer
93
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1
answer
Design and Contrast Matrix for Linear Model. To Combine or not to Combine?
limma design and contrast matrix design matrix contrast matrix written 19 days ago by mikhael.manurung • 10 • updated 19 days ago by James W. MacDonald ♦ 48k
1
vote
1
answer
50
views
1
answer
How to apply KEGG enrichment analysis to the overlap of multiple contrasts in MArrayLM fit?
limma kegg written 19 days ago by antoinefelden • 10 • updated 19 days ago by Gordon Smyth ♦ 35k
1
vote
1
answer
61
views
1
answer
Visualise gene set analysis plot
limma gene set analysis gene set enrichment written 19 days ago by jaynishshah • 0 • updated 19 days ago by Gordon Smyth ♦ 35k
3
votes
2
answers
126
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2
answers
Batch correction when only some subjects have replicates across batches
limma rna-seq batch effect written 21 days ago by Mike A • 10 • updated 19 days ago by Peter Langfelder • 1.6k
1
vote
1
answer
70
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1
answer
the results of logFC is base e (log(FC,base=exp(1)) or base 2 (log2FC) ,is logFC same as log2FC in edgeR?
limma edger logfc written 22 days ago by ZihaoXing • 0 • updated 22 days ago by Gordon Smyth ♦ 35k
5
votes
1
answer
103
views
1
answer
Voom transformation from counts and normalization to negative values
rnaseq limma statistics voom tcga written 23 days ago by Beginner • 50 • updated 23 days ago by Ryan C. Thompson ♦ 6.9k
0
votes
1
answer
54
views
1
answer
Error in data.frame for limmaCtData function
limma software error data.frame written 27 days ago by azmir004 • 0 • updated 27 days ago by Gordon Smyth ♦ 35k
6
votes
2
answers
95
views
2
answers
Incorporating subject ID as random effect for repeated measures RNA-Seq analysis
limma rna-seq repeated measures mixed model written 28 days ago by mikhael.manurung • 10 • updated 28 days ago by Gordon Smyth ♦ 35k
3
votes
1
answer
184
views
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 4 weeks ago by svlachavas • 610 • updated 4 weeks ago by Gordon Smyth ♦ 35k
0
votes
2
answers
103
views
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 4 weeks ago by seblatt • 0 • updated 4 weeks ago by Robert Castelo • 2.2k
0
votes
1
answer
84
views
1
answer
mroast/fry with gene weights for most or all genes
limma mroast fry written 5 weeks ago by maltethodberg • 100 • updated 4 weeks ago by Gordon Smyth ♦ 35k
0
votes
1
answer
67
views
1
answer
Limma analysis combining twins pairs and unpaired controls
rnaseq limma twin analysis written 4 weeks ago by kalletrontti • 0 • updated 4 weeks ago by Aaron Lun • 21k
0
votes
1
answer
60
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1
answer
Visualization of analysis of multiple cell lines
limma plotmds cell lines written 4 weeks ago by Alexander Az. • 0 • updated 4 weeks ago by Gordon Smyth ♦ 35k
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