Thanks Colin, That would be great! I tried one other test also after my email. I loaded the old version of annaffy that worked under R2.5 into R2.7. The same "bad" behaviour resulted. I suspected the problems came from the merge commands .... Which is probably less commonly used with annaffy... However my tested included using exactly the same data_table object in both R versions just before using the saveHTML command (saved workspace under R2.5 loaded into R2.7 and just the saveHTML was run : same effect). Hope that info is of some use... Attached is the output. Anyway here is the guts: THE INPUT is the table "top": > top CHR US UK UK_US posn RS785702 5 6.173e-03 3.217e-253 4.628e-03 122480032 RS258415 12 NA 1.109e-199 NA 27908789 RS7006137 8 9.323e-119 4.770e-197 5.180e-205 132952261 > rownames(top) [1] "RS785702" "RS258415" "RS7006137" > colnames(top) [1] "CHR" "US" "UK" "UK_US" "posn" R COMMANDS: library(annaffy) ############ a table filename<- "topUK50.html" title <- "Top 50 in UK : with UK+US and US for comparison " newURLs<-lapply(sub("RS","",rownames(top)),function(x) paste('', sep = "", collapse = NULL) ) newURLs<-paste(newURLs,rownames(top),sep="",collapse=NULL) newURLs<-unlist(newURLs) acc_table<-aafTable("SNP",items=list(newURLs),colnames="SNP") #tried diff versions of this line but it didn't work.. chr_table <-aafTable("Chr"=as.character(top[,"CHR"])) loc_table <-aafTable("Posn"=as.character(top[,"posn"])) UK_table <-aafTable("UK"=signif(as.numeric(top[,"UK"]),3 )) UK_US_table<- aafTable("UK_US"=signif(as.numeric(top[,"UK_US"]),3 )) US_table<- aafTable("US"=signif(as.numeric(top[,"US"]),3 )) data_table <- merge(acc_table,chr_table) data_table <- merge(data_table,loc_table) data_table <- merge(data_table,UK_table) data_table <- merge(data_table,UK_US_table) data_table <- merge(data_table,US_table) saveHTML(data_table,filename,title) Cheers Paul PS sessionInfo() provided in the first email of this thread Cheers Paul ________________________________ From: Colin A. Smith [mailto:colin@colinsmith.org] Sent: Tuesday, 9 October 2007 3:58 AM To: bioconductor at stat.math.ethz.ch Cc: Paul Leo Subject: Re: [BioC] annaffy - saveHTML changed behaviour in newer versions Paul- R 2.6.0 is a lot more picky about the kinds of R variables for which it will do S4 methods dispatch. To be able to figure out the problem, I need to see the exact sequence of commands you used to generate the aafTable object. -Colin On Oct 8, 2007, at 3:00 , bioconductor-request at stat.math.ethz.ch wrote: Date: Mon, 8 Oct 2007 11:18:07 +1000 From: "Paul Leo" <p.leo@uq.edu.au> Subject: [BioC] annaffy - saveHTML changed behaviour in newer versions To: <bioconductor at="" stat.math.ethz.ch=""> Message-ID: < DE3D1F203DAF7A4CB259560D2801DF8B0166BB44 at UQEXMB2.soe.uq.edu.au> Content-Type: text/plain HI I use annaffy to make nice HTML tables of various forms of data, but save "saveHTML" has changed and the wheels have fallen off. I'm not sure is the authors intended the change in functionality or not? -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: topUK50_R2.6output.html Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20071009/ a487f3e6/attachment.pl -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: topUK50_R2.5output.html Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20071009/ a487f3e6/attachment-0001.pl