[BioC] annotation

[James W. MacDonald]

Hi Morten,

Wouldn't it be easier to do this using annaffy to make the HTML table as 
well? For any Affy chip that has an annotation package I think the 
annaffy package is much easier to use than the annotate package. You 
might also look at affycoretools in the devel repository. You could do 
this using one line of code with the limma2annaffy() function.

Hi Marco,

The htmlpage() function in annotate currently allows you to make 
hyperlinks to Entrez Gene, Affy, UniGene, OMIM, and SwissProt. See 
?getQuery4UG for more information. In addition, it is simple to make 
more getQuery4XX() functions that will create hyperlinks to other online 
databases if these are not to your liking.

Best,

Jim



Morten Mattingsdal wrote:
> 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
>>
>>_______________________________________________
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>
> 
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor


-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.