Entering edit mode
Jenny Bryan
▴
110
@jenny-bryan-949
Last seen 9.7 years ago
First, many thanks to those behind this method and package. I have
gcrma 1.1.0.
I've experienced a problem with just.gcrma and I'm pretty sure it's
not user error. I am pre-computing the probe affinity info and
passing it via the "affinity.info" argument. The "just.gcrma" function
is not passing that affinity info on to "fast.bkg" and/or "mem.bkg".
Failure with pre-computed affinity info:
> moe430a.ai <- compute.affinities("moe430a")
> jeset.A <-
+ just.gcrma(filenames = paste(where.am.i, "data/celfiles/",
+ chip.details.sel[take.me,
+ "chip.names"],
+ sep=""),
+ phenoData = pD.A[1:4,],
+ affinity.info = moe430a.ai,
+ type="affinities")
Adjusting for optical effect.....Done.
Error in sample(1:length(pms[index.affinities, ]), 25000) :
Object "index.affinities" not found
Success when allowing just.gcrma to re-compute the affinity info:
> jeset.A <-
+ just.gcrma(filenames = paste(where.am.i, "data/celfiles/",
chip.details.sel[take.me,
+ "chip.names"],
+ + sep=""),
+ phenoData = pD.A[1:4,],
+ type="affinities")
Computing affinities..Done.
Adjusting for optical effect.....Done.
Adjusting for non-specific binding....Done.
Normalizing
Calculating Expression
Success with pre-computed affinity info, with a slight fix in
just.gcrma:
> jeset.A2 <-
+ jb.just.gcrma(filenames = paste(where.am.i, "data/celfiles/",
+ chip.details.sel[take.me,
+ "chip.names"],
+ sep=""),
+ phenoData = pD.A[1:4,],
+ affinity.info = moe430a.ai,
+ type="affinities")
Adjusting for optical effect.....Done.
Adjusting for non-specific binding....Done.
Normalizing
Calculating Expression
The statements inside "if (needaff & is.nullaffinity.info)) {...}
could be replaced with:
if (needaff) {
if (is.nullaffinity.info)) {
if (verbose)
cat("Computing affinities.")
affinity.info <- compute.affinities(cdfName, verbose = verbose)
int.aff.calc <- TRUE # is the garbage collection important?
if (verbose)
cat("Done.\n")
} else int.aff.calc <- FALSE # allows garbage collection below
pm.affinities <- pmaffinity.info)
mm.affinities <- mmaffinity.info)
index.affinities <- which(!is.na(pm.affinities))
pm.affinities <- pm.affinities[index.affinities]
mm.affinities <- mm.affinities[index.affinities]
if (int.aff.calc) {
rmaffinity.info)
gc()
}
}
--
Jenny Bryan, Ph.D.
*----------------------------------*
* Assistant Professor *
* Department of Statistics and *
* the Michael Smith Laboratories *
* University of British Columbia *
*----------------------------------*
333-6356 Agricultural Road
Vancouver, BC V6T 1Z2 Canada
http://hajek.stat.ubc.ca/~jenny/
tel: 604.822.6422
fax: 604.822.6960
email: jenny@stat.ubc.ca
