[BioC] affylmGUI 1.10.4 fixes 3 errors in Bioconductor release version

[Keith Satterley]

To affylmGUI users,

I have sent version 1.10.4 of affylmGUI to the current release of Bioconductor. 
There were three small changes as follows:
1. References to Digestion changed to Degradation. Changed Menu Item name and 
function names. See Bioconductor emails from Gordon Smyth/Robert Gentleman 
around December 6th. 2006 confirming this choice of words.

2. Fixed a bug in Normalize.R introduced in 1.10.1 - bracket misplaced as shown 
below:
Replaced this line
Try(write.table(NormalizedAffyData.exprs),file=FileName,sep="\t",quote=FALSE,col.names=NA)
with
Try(write.table(NormalizedAffyData.exprs,file=FileName,sep="\t",quote=FALSE,col.names=NA))

3. Error on console when HTML report was to be created. It read:
   "Error in get(x, envir, mode, inherits) : variable "HTMLenv" was not found"
Modify htmlreport.R
replace:
   try(assign(".HTML.graph", TRUE, env = get("HTMLenv", envir = .GlobalEnv)))
with:
   if (exists("HTMLenv",where=".GlobalEnv",mode="environment")){
     try(assign(".HTML.graph", TRUE, env = get("HTMLenv", envir = .GlobalEnv)))
   }#end of if (exists("HTMLenv",where=".GlobalEnv",mode="environment"))

I shall update tomorrow the Bioc-devel version (1.11.4) to be the same as 1.10.4 
on the release version.

cheers,

Keith