[BioC] GEOquery and parsing SOFT files

[Wacek Kusnierczyk]

Sean Davis wrote:
> On Tue, May 26, 2009 at 3:21 AM, Wacek Kusnierczyk <
> Waclaw.Marcin.Kusnierczyk at 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.
>   

i didn't mean "essential for my task", but rather "useful given that gse
matrix files are available".  that is, if there are good reasons to
download and parse soft files, the package may need a fix --
irrespectively of what my own study is.

vQ