Question: pathway analysis package
0
gravatar for Josephine.Liang@uchsc.edu
15.0 years ago by
Hi, Robert and Saurin; In the release 1.5, I find the KEGGSOAP, RBGL and Rgraphiviz packages, but not KEGG? Any pointers Thanks Josephine Saurin D. Jani wrote: >Hi, > >Regarding Pathway analysis: > >In bioconductor when I load: library(KEGG) > >I can do this: >kegg <- as.list(rae230aPATH2PROBE); > >and I can generate heatmap of pathway probes which are involved in my DEgenes >so, I can see which genes are up and down in perticular pathway. > >how can I use interaction data extracted from human BioCarta pathways for my >differentially expressed genes? > >if anyone has done please let me know... > > >Thank you, >Saurin > > > >
rbgl keggsoap • 571 views
ADD COMMENTlink modified 15.0 years ago by Sean Davis21k • written 15.0 years ago by Josephine.Liang@uchsc.edu60
Answer: pathway analysis package
0
gravatar for John Zhang
15.0 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
KEGG is an annotation package that can be obtained by > library(reposTools) > install.packages2("KEGG") or install.packages2("KEGG", develOK = TRUE)
ADD COMMENTlink written 15.0 years ago by John Zhang2.9k
Answer: pathway analysis package
0
gravatar for Sean Davis
15.0 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
It is a metadata package. http://www.bioconductor.org/data/metaData.html Sean On Dec 17, 2004, at 11:34 AM, Josephine Liang wrote: > Hi, Robert and Saurin; > > In the release 1.5, I find the KEGGSOAP, RBGL and Rgraphiviz packages, > but not KEGG? Any pointers > > > Thanks > Josephine > > Saurin D. Jani wrote: > >> Hi, >> >> Regarding Pathway analysis: >> In bioconductor when I load: library(KEGG) >> >> I can do this: >> kegg <- as.list(rae230aPATH2PROBE); >> >> and I can generate heatmap of pathway probes which are involved in my >> DEgenes >> so, I can see which genes are up and down in perticular pathway. >> >> how can I use interaction data extracted from human BioCarta pathways >> for my >> differentially expressed genes? >> >> if anyone has done please let me know... >> >> >> Thank you, >> Saurin >> >> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENTlink written 15.0 years ago by Sean Davis21k
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