[BioC] annotation

[Morten Mattingsdal]

Hi Marco,
Aha... ive build some code with uses the "annotation" package and the 
htmlpage function... this creates a hyperlink to entrez gene at ncbi. My 
code requires a LIMMA toplist ("top"), but it should be very doable if 
you have a character vector of affymetrix probe ID:

# html page of Affymetrix LIMMA top list with Entrez Gene hyperlinks
probe<-top[,1]
description<-aafDescription(as.character(probe),"hgu133plus2")
DE<-getText(description)
m<-top[,2]
p<-top[,5]
p_adj=top[,6]
b<-top[,7]
M<-round(m,2)
P<-round(p,5)
P_adj=round(p_adj,2)
B<-round(b,5)
xx<-mget(probe,ifnotfound="NA",hgu133plus2ACCNUM)
acc<-as.data.frame(cbind(xx))
ll <- getLL(probe,data="hgu133plus2")
symbol <- getSYMBOL(probe,data="hgu133plus2")
res<-data.frame(cbind(unlist(probe)),cbind(unlist(symbol),unlist(acc),unlist(DE),unlist(M),unlist(P),unlist(P_adj),unlist(B)))
names(res)<-cbind("Probe","Symbol","Acc","Description","log2 Ratio","p value","adjusted P value","B")
htmlpage(ll,filename="Results_lps_choe.html",title="Positive - Negative, sorted by M>1",othernames=res,
table.head=c(("Entrez ID"),names(res)),table.center=TRUE)



hope this can be usefull
morten




> About the biomaRt package, thank you this solved my problem
>
> About the second point, probably my question was not clear, I try to
> better explain myself.
> When I annotate my gene list I use the annotate package and when I
> produce the html page the probset are linked to the netaffix page
> (https://www.affymetrix.com/LinkServlet?&probeset=200629_at).
> I do not like the affymetrix  page ands I  would like to create a link
> to another page, do you have suggestion for this?
>
> Thanks Marco
>
> On 20/03/06, Morten Mattingsdal <morten.mattingsdal at student.uib.no> wrote:
>   
marco fabbri wrote:
> I ahve two questions:
> 1.
> I am working with  human chip hgu133plus2.0 and mouse chip mgu74av2.
> I would like to annotate my lists with the correspondent hortologous
> in the other species.
>   
have a look at the getHomolog function in the biomaRt package. Could be 
usefull
> 2.
> when I annotate my list I create html pages, I would like to add a
> simple link like  www.mywebpage.pobename=probest
> where probset is the name of the probset that to be annotated.
>
>   
your link is dead :(
> Thank you
>
> Marco
>
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