On Tue, May 26, 2009 at 3:21 AM, Wacek Kusnierczyk <
Waclaw.Marcin.Kusnierczyk@idi.ntnu.no> wrote:

> Sean Davis wrote:
>
> [...]
> > Thanks, Wacek, for the report.  This is a known issue and GEOquery could
> > probably be smarter than it currently is; I have not changed that code in
> q
> > while since GEO began using GSE Matrix files.  You could try using
> > GSEMatrix=TRUE, as the documentation suggests.  You will find that will
> deal
> > with your speed issues.
> >
> >
>
> thanks.  if parsing soft files is no longer essential, it makes little
> sense for me to delve into the implementation details;  otherwise, i
> could try to find a spot for improvement.  what's your opinion?
>

If all you need are the "expression" values from GSE entities, then the GSE
Matrix will be faster, no matter the implementation, because it is smaller.
But I really do not know what your needs are, so I cannot answer your
question directly.

Sean

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