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limma 2x2 factorial contrast.matrix
limma
weaver
limma
weaver
14.0 years ago
Ben Nota
▴ 10
0
votes
3
replies
972
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interaction term contrast in Weaver mutant example of LIMMA manual
limma
weaver
limma
weaver
updated 14.7 years ago by
James W. MacDonald
65k • written 14.7 years ago by
Erika Melissari
▴ 250
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0
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1.2k
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subscript out of bounds halting error when Sweaving with weaver And GOstats' HyperGTest
GO
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GO
weaver
15.6 years ago
Elliot Kleiman
▴ 150
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1
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2.0k
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Limma user’s guide example data sets
Microarray
limma
limmaGUI
weaver
Microarray
limma
limmaGUI
weaver
updated 15.9 years ago by
Wang, Jixin
▴ 130 • written 15.9 years ago by
Keith Satterley
▴ 450
0
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972
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Limma user’s guide example data sets
Microarray
limma
weaver
Microarray
limma
weaver
15.9 years ago
Wang, Jixin
▴ 130
0
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0
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890
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Limma - using both array and spot weights in lmFit
Genetics
limma
weaver
Genetics
limma
weaver
17.0 years ago
Gordon Smyth
50k
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0
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823
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Advice on how to compare two different sources on cDNA
limma
weaver
limma
weaver
17.3 years ago
Marcelo Laia
▴ 450
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1
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804
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limma example Weaver Data
limma
weaver
limma
weaver
18.9 years ago
Gordon Smyth
50k
0
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3
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1.3k
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limma example Weaver Data
limma
weaver
limma
weaver
updated 18.9 years ago by
Gordon Smyth
50k • written 19.0 years ago by
Wenbin Liu
▴ 100
0
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0
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955
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Controls and duplicate correlation
limma
weaver
limma
weaver
19.0 years ago
lepalmer@notes.cc.sunysb.edu
▴ 40
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3
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1.2k
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design in mixed ref and dye-swap experiment
limma
weaver
limma
weaver
updated 19.1 years ago by
Gordon Smyth
50k • written 19.1 years ago by
Silvano Piazza
▴ 50
0
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0
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2.4k
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limma design matrix
GO
limma
PROcess
weaver
GO
limma
PROcess
weaver
20.2 years ago
Gordon Smyth
50k
0
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2
replies
1.0k
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limma missing files
weaver
weaver
updated 21.0 years ago by
Gordon Smyth
50k • written 21.0 years ago by
Dick Beyer
★ 1.4k
13 results • Page
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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