[BioC] Problem with mgu74av2LOCUSID environment

[John Zhang]

It appears that your first argument (vav2onlyLI) to ll.htmlpage is a list while 
ll.htmlpage is expecting a vector. I was able to create a table with correct ids 
by unlisting vav2onlyLI (after replacing the unknow 
RES.lm[RES.lm[,"eff"]=="vav2","gene"] with a set of probe ids. It would be nice 
if you could provide example code that can be run directly next time).

 
>From: Fátima Núñez Mangado <fnunez at usal.es>
>To: <bioconductor at stat.math.ethz.ch>
>Date: Wed, 5 May 2004 17:34:47 +0200
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>Subject: [BioC] Problem with mgu74av2LOCUSID environment
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>Dear all,
>
>I have recently changed my version of R form 1.8.1 to 1.9.0.
>
>I have been trying to produce a few html pages with some of my results
>and up to now I have had no problems. See below:
>
>Locus ID  Gene Symbol  Affy ID  Pvalue  FC  
>17865  Mybl2 100023_at 0 1.68 
>12035  Bcat1 100026_at 0 1.58 
>22271  Upp1 100030_at 0 1.54
>.
>.
>.
>
>Where the first column is a hyperlink to LocusLink obtained with the
>following piece of code:
>
>library(annotate)
>library(mgu74av2)
>
> vav2onlyNames <- RES.lm[RES.lm[,"eff"]=="vav2","gene"]
>
>
> vav2onlyLI <- multiget(vav2onlyNames, env = mgu74av2LOCUSID)
>
> 
> vav2onlySYM <- multiget(vav2onlyNames, env = mgu74av2SYMBOL)
>
> 
> vav2onlyRes <- data.frame (unlist(vav2onlySYM))
>
> 
>
>ll.htmlpage(vav2onlyLI, filename = "Vav2 genes.html", 
>	        title = "Vav2 genes", othernames =
>data.frame(vav2onlyRes,
>vav2onlyNames,RES.lm[RES.lm[,"gene"]%in%vav2onlyNames,
>                                               c("FC","Pval")]), 
>		  table.head = c("Locus ID", "Gene Symbol", "Affy ID",
>"FC","Pval",), table.center = TRUE)
>
>
>The problem has begun when I have started using the R version 1.9.0.
>Instead of the html table format I have detailed before - and using the
>exact same code, I obtain the following:
>
>Locus ID  Gene Symbol  Affy ID  Pval FC    
>as.integer(17865)  Mybl2 100023_at 0 1.68
>as.integer(12035)  Bcat1 100026_at 0 1.58
>as.integer(22271)  Upp1 100030_at 0 1.54
>.
>.
>
>where the first column stops being a useful LocusLink hyperlink.
>
>I am not totally sure this is the correct list to share my concerns, if
>not, I apologize in advance and I hope someone can give me an idea of
>what is going on or direct me to the appropriate place where I could
>receive help.
>
>Thanx a lot,
>
>Fatima
>
>---
>Fátima Núñez
>Centro de Investigación del Cáncer, CIC
>Universidad de Salamanca-CSIC
>Campus Unamuno
>37007 Salamanca
>
>Phone:  + 34 923 294802
>Fax:    + 34 923 294795
>E-mail: fnunez at usal.es
>
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Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084