On Tue, 2002-06-11 at 12:31, Joshua Betcher wrote:
> I have been going through the code for this package and I have a few
> questions and comments:
>
> 1) For normalize.Plob.loess, slot names that do not exist are used.
>
> 2) As I have looked through the help files there does not appear to
be any
> examples of the use of the read.cdfile, read.affy, etc.. Does
anyone happen
> to have example files that these functions could be used on?
>
> 3) Is there equivalent function to optim in splus? It was
mentioned in the
> code that maybe nlminb could be used; could someone explain this
further?
>
> Thanks everyone for your help
> Josh
>
Let me add 2 bugs for normalize.Plob.invariantset:
1) When called from express(), it dumps the following error:
Error in normalize.Plob.invariantset(object, ...) :
unused argument(s) (span ...)
Easy fix is to add the optional "three dots" argument.
2) Once 1 is fixed, normalize.Plob.invariantset has trouble with the
result of approx() function, which by default returns NA, when trying
to
approximate outside of the initial range(rule=1). Easy fix is to set
the
value of parameter rule to 2. In this case approx will return
min(y)/max(y) accordingly.
I use affy_1.1.0.tar.gz, R-1.5.0 on RH 7.2 Linux P3 machine.
Peter Dimitrov
P.S. This is the code of normalize.Plob.invariantset that I currently
use:
"normalize.Plob.invariantset" <-
function (container, prd.td = c(0.003, 0.007), progress =
FALSE,...)
{
nc <- ncol(pm(container))
np <- nrow(pm(container))
refindex <- trunc(median(rank(apply(pm(container),2,mean))))
for (i in (1:nc)[-refindex]) {
if (progress)
cat("normalizing array", attr(container[[i]], "name"),
"...")
tmp <- normalize.invariantset(pm(container)[, i],
pm(container)[, refindex], prd.td)
pm(container)[, i] <- as.numeric(approx(tmp$n.curve$y,
tmp$n.curve$x, xout =
container@pm[, i])$y,
rule=2)
mm(container)[, i] <- as.numeric(approx(tmp$n.curve$y,
tmp$n.curve$x, xout =
mm(container)[, i])$y,
rule=2)
container@notes <- "normalized by invariant set"
if (progress)
cat("done.\n")
}
return(container)
}
