[BioC] agcdf / atgenome1probe

[Laurent Gautier]

The affy package contains a data.frame where such oddities are stored.

Originally, one only had to add entries to a flat file to have things fixed.
I looked at it on a recent version of the 'affy' package, and I found 
out that some changes were made recently (*) in that respect, and that
they are not very practical.

- Temporary (but quick) fix: have your own version of the function 
'mapCdfName' in a separate file (to source after loading the package)

#####
data(mapCdfName)
  cleancdfname <- function (cdfname, addcdf = TRUE)
{
     if (!is.character(cdfname))
         stop(paste("invalid CDF name:", cdfname))
     if (nchar(cdfname)[1] == 0)
         stop("supplied cdf name has zero length")
     i <- match(cdfname, mapCdfName$inCDF)
     if (is.na(i)) {
         tmp <- tolower(cdfname)
         tmp <- gsub("_", "", tmp)
         tmp <- gsub("-", "", tmp)
         tmp <- gsub(" ", "", tmp)
         if (addcdf)
             tmp <- paste(tmp, "cdf", sep = "")
     }
     else {
         tmp <- mapCdfName$inBioC[1]
     }
     return(tmp)
}
####
Now you can
edit(mapCdfName)
and add your findings with the naming scheme (and report to us so
we can improve what is in the default 'mapCdfName').

- Long(er) term fix: have the 'data(mapCdfName)' inside the function
'mapCdfName' removed (why load over and over again the very same data 
set at each function call ?!?!), and have 'data(mapCdfName)' moved the
the .FirstLib call.


hth,


L.

(*) Well, I should say 'changes were made since the last time I looked 
at that'




Matthew Hannah wrote:
> Hi,
> 
> The metadata for the atgenome array has different names, so when you try
> gcrma it's looking for agprobe, rather than the atgenome1probe that is
> installed. Could someone fix this please, or offer a fix of how to point
> justGCRMA to the correct library in the meantime.
> 
> Cheers,
> Matt
> 
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