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graphite
•
reset
2
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3
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2.6k
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Goseq analysis with Biocarta, Reactome, and NCI pathways?
goseq
graphite
9.2 years ago • updated 7.4 years ago
b.nota
▴ 360
0
votes
11
replies
2.6k
views
"graphite" Biocarta 'native' graphs different from Biocarta web site?
Transcription
Pathways
Leukemia
graphite
Transcription
Pathways
Leukemia
graphite
11.9 years ago
Hamid Bolouri
▴ 90
0
votes
3
replies
1.9k
views
runSPIA() in graphite package
Pathways
Breast
siggenes
PROcess
cycle
graphite
Pathways
Breast
siggenes
PROcess
cycle
updated 11.2 years ago by
Enrica
▴ 20 • written 11.2 years ago by
array chip
▴ 420
1
vote
2
replies
1.9k
views
Question on graphite/SPIA; extracting DE gene list
graphite
spia
runSPIA
updated 5.3 years ago by
Bioconductor Community
0 • written 9.2 years ago by
rgamini
• 0
5
votes
4
replies
1.8k
views
Reactome pathways in ReactomeDB/graphite
reactomepa
reactome
graphite
updated 7.3 years ago by
gabriele.sales
▴ 100 • written 7.3 years ago by
i.sudbery
▴ 40
0
votes
1
reply
1.7k
views
pathway analysis by SPIA using SPIA package vs graphite package
Pathways
SPIA
cycle
graphite
Pathways
SPIA
cycle
graphite
10.3 years ago
array chip
▴ 420
1
vote
2
replies
1.6k
views
graphite KEGG pathway list vs KEGG pathway list
graphite
updated 9.1 years ago by
gabriele.sales
▴ 100 • written 9.2 years ago by
rgamini
• 0
1
vote
4
replies
1.5k
views
Indirect path in KEGG, activation or inhibition?
bioconductor
graphite
kegg
pathway analysis
updated 7.2 years ago by
gabriele.sales
▴ 100 • written 7.2 years ago by
haoran.chen
• 0
1
vote
3
replies
1.5k
views
graphite functions missing, installed version is out of date
graphite
bioclite
8.9 years ago
mhlinder
• 0
0
votes
4
replies
1.4k
views
graphite and PoTRa
graphite
potra
6.2 years ago • updated 6.1 years ago
genomic8328
▴ 10
1
vote
2
replies
1.4k
views
KEGG data error?
bioconductor
graphite
pathway analysis
updated 7.2 years ago by
gabriele.sales
▴ 100 • written 7.2 years ago by
haoran.chen
• 0
0
votes
2
replies
1.3k
views
edge-less pathways in graphite
graphite
graphite
updated 12.0 years ago by
Paul Shannon
▴ 750 • written 12.0 years ago by
Hamid Bolouri
▴ 90
0
votes
0
replies
1.2k
views
graphite biopax conversion code?
Pathways
graphite
Pathways
graphite
10.0 years ago
Ryan C. Thompson
★ 7.9k
3
votes
2
replies
1.2k
views
Error installing graphite
graphite
updated 5.5 years ago by
gabriele.sales
▴ 100 • written 5.5 years ago by
Lluís Revilla Sancho
▴ 730
0
votes
2
replies
1.1k
views
graphite package SSL certificate
graphite
2.4 years ago • updated 2.3 years ago
x
• 0
0
votes
2
replies
820
views
Direct interactions in graphite ?
graphite
interaction
updated 4.0 years ago by
gabriele.sales
▴ 100 • written 4.1 years ago by
emisecherre
• 0
0
votes
3
replies
107
views
Couldn't connect to server while using "pathways"
graphite
updated 1 day ago by
Michael Love
42k • written 1 day ago by
fduguchunhui
• 0
17 results • Page
1 of 1
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Replies
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
Gordon Smyth
50k
The formula given in the original question is correct and yours is not. Your formula isn't even constrained to be between 0 and 1. Here is …
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square?
by
nbay13
• 0
A little late to the party, but I found that using the equation you specified, the p-values are actually slightly off from base R's `t.test…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Answer: Extremely small p-values using Limma for proteomic data
by
James W. MacDonald
65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
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