[BioC] Problem with mgu74av2LOCUSID environment

[Fátima Núñez Mangado]

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