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piano
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9
votes
7
replies
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Single Sample GSEA (ssGSEA) and dynamic range of expression
ssgsea
gsva
piano
egsea
updated 5 months ago by
amin8w
▴ 10 • written 6.8 years ago by
sina.nassiri
▴ 130
3
votes
8
replies
2.4k
views
Error: 'exprs<-' is not an exported object from 'namespace:affy'
affy
limma
piano
updated 4.6 years ago by
James W. MacDonald
65k • written 4.6 years ago by
abolfazl.nikakhtar
• 0
0
votes
5
replies
2.3k
views
loadGSC() Piano package
piano
updated 9.1 years ago by
Leif Väremo
▴ 70 • written 9.1 years ago by
nonCodingGene
▴ 10
0
votes
3
replies
1.7k
views
piano runGSA with input from DESEQ2
deseq2
gene ontology
piano
7.5 years ago
simonp.snoeck
• 0
0
votes
9
replies
1.7k
views
unable to load rsbml for piano reporter metabolite analysis
rsbml
piano
libsbml
gene set enrichment analysis
updated 5.5 years ago by
Michael Lawrence
★ 11k • written 5.5 years ago by
jan.strauss
• 0
3
votes
3
replies
1.6k
views
Error while running piano's runGSA
piano
runGSA
updated 7.9 years ago by
Leif Väremo
▴ 70 • written 7.9 years ago by
rubi
▴ 110
2
votes
4
replies
1.3k
views
Running time of piano's runGSA
piano
runGSA
runtime
updated 7.3 years ago by
Leif Väremo
▴ 70 • written 7.3 years ago by
rubi
▴ 110
2
votes
2
replies
1.2k
views
Using GeneSetCollection objects of GSEABase in piano package
piano
gseabase
7.3 years ago
Lluís Revilla Sancho
▴ 730
0
votes
1
reply
1.2k
views
Mixing list from Piano package output
Piano
List
updated 9.0 years ago by
Leif Väremo
▴ 70 • written 9.0 years ago by
nonCodingGene
▴ 10
3
votes
2
replies
1.1k
views
How is microarray normalization done in PIANO?
piano
microarray
updated 6.5 years ago by
James W. MacDonald
65k • written 6.5 years ago by
rf
• 0
10 results • Page
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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. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
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…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga
by
Michael Love
41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
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
A: Print Differentially Expressed Exons From Dexseq Results
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