[BioC] trouble with rhdf5 and hdf5.datasets
Byron Ellis
bellis@hsph.harvard.edu
Sun, 21 Jul 2002 10:01:58 -0400 (EDT)
Whoops, didn't scroll down that last bit...did you try mad[["chip1"]]?
Byron Ellis (bellis@hsph.harvard.edu)
"Oook" - The Librarian
Please finger bellis@hsph.harvard.edu for PGP keys
On Sun, 21 Jul 2002, Laurent Gautier wrote:
> Dear all,
>
> I observed unexplainable things with rhdf5. I do not
> know if they could be avoided.
>
> I am trying to access datasets in a group using the
> function 'do.call' with "$" (since the name of the
> dataset will only be known at run-time)... and I have
> a hard time with that (example below). Does anybody
> have experience with that ?
>
>
> ## example from the help file
> > mad <- hdf5.open("microarray.h5")
> > # Create a new group inside the file
> > hdf5.group(mad,"chip1")
> > hdf5.dataset(mad$chip1,"raw", dim=c(534,534))
> >
> > raw <- mad$chip1$raw
> > for(i in 1:534)
> + { raw[i,1:534] <- runif(534) }
>
> >
> > do.call("$", list("mad", "chip1"))
> NULL
>
> # uh, uh....
>
>
> > mad$chip1
> Name Type Date Comment
> [1] raw Dataset 21/07/2002 16:26
>
> # let's try again...
>
> > do.call("$", list("mad", "chip1"))
> NULL
> > mad
> Name Type Date Comment
> [1] chip1 Group
>
> # show stopper
>
> > mad[[1]]
> Segmentation fault
>
>
>
>
>
> Thanks,
>
>
>
>
> Laurent
>
>
>
>
>
>
> --
> --------------------------------------------------------------
> Laurent Gautier CBS, Building 208, DTU
> PhD. Student DK-2800 Lyngby,Denmark
> tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent
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