[BioC] "Size" in summary() of "hyperGTest()

[Sergei Manakov]

Hello Robert,

Thanks for your reply. You are right, indeed I have used conditional =
TRUE, and that is the reason why "Size" differs. Sorry about that, I
should have guessed that myself. However, I find the description of
the option "conditional" rather short in the Vignette. Could you
please maybe just in a few sentences explain what it exactly it does?
That would be very helpful.

thanks,
Sergei



2009/2/18 Robert Gentleman <rgentlem at fhcrc.org>:
> Hi Sergei,
>   Sorry to be so slow in getting back to you.
>
> On Tue, Feb 17, 2009 at 3:40 AM, Sergei Manakov <manakov at ebi.ac.uk> wrote:
>> Hello,
>>
>> I assume that "Size" column in the table generated by summary() of
>> "GOHyperGResult" object produced by hyperGTest() function from
>> "GOstats" package is the total size of a given GO category.
>
>  Not necessarily, it will depend on a number of factors (some of them
> depend on parameters you have set).
>  So, first, it does depend on the gene universe, but it also will
> vary if you have set conditional=TRUE, as in that case any significant
> children are excluded - which is what conditional means, in this
> setting.  I believe you will find that they are always identical if
> you set conditional=FALSE, but please let me know if not, and in that
> case, if you could follow the posting guide and provide details such
> as sessionInfo() and a small example, I can try to be more helpful.
>
>  best wishes
>   Robert
>>
>> In this regard I am puzzled why values in this field are slightly
>> different for the same GO categories when I run the  hyperGTest() on
>> different query gene lists, even when using the same Universe.
>>
>> I would be grateful for any suggestions.
>>
>> thanks,
>> Sergei
>>
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>>
>
>
>
> --
> Robert Gentleman, PhD
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
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>