[BioC] problem with "just.gcrma" and a fix

[James W. MacDonald]

Jenny Bryan wrote:
> Thanks for your reply.  My inspiration for using the pre-computed
> affinities was the Example given in the gcrma help file (and the
> slowness of my machine!). I'm not where I can test this right now, but
> given your response, maybe that example would fail too?
> 
Yep. As you already noted, the fix is to decouple the following if 
statement:

if (needaff & is.null(affinity.info)) {
        if (verbose)
            cat("Computing affinities")
        affinity.info <- compute.affinities(cdfName(object),
            verbose = verbose)
        if (verbose)
            cat("Done.\n")

         pm.affinities <- pm(affinity.info)
         mm.affinities <- mm(affinity.info)
         index.affinities <- which(!is.na(pm.affinities))
         pm.affinities <- pm.affinities[index.affinities]
         mm.affinities <- mm.affinities[index.affinities]
         rm(affinity.info)
         gc()
     }


To:

  if (needaff) {
         if (is.null(affinity.info)) {
             if (verbose)
                 cat("Computing affinities.")
             affinity.info <- compute.affinities(cdfName, verbose = verbose)
             if (verbose)
                 cat("Done.\n")
         }
         pm.affinities <- pm(affinity.info)
         mm.affinities <- mm(affinity.info)
         index.affinities <- which(!is.na(pm.affinities))
         pm.affinities <- pm.affinities[index.affinities]
         mm.affinities <- mm.affinities[index.affinities]
         rm(affinity.info)
         gc()
     }

Something similar is required for gcrma.

Best,

Jim



-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109