[BioC] plier package

[Michal Blazejczyk]

Hello,

In fact, I looked at this in the past, and I found that
the parameters do not translate all that well...

The "Guide to Probe Logarithmic Intensity Error (PLIER)
Estimation" from Affymetrix web site mentions four types
of normalization: PM-MM, PM-B, PM Only, and "MM treated
as additional PM".  Function justPlier() in Bioconductor
has on the other hand 'separate', 'pmonly', 'mmonly', and
'together'.  What is the relationship?

The function also has a whole bunch of parameters that
Affy documentation doesn't elude to directly.  This is in
sharp contrast to algorithms like RMA that have only a few
parameters that are easy to understand.

A better explanation would be most welcome...

I think this may be causing justPlier() more problems on
the psychological level of users.  I've heard statisticians
saying that they won't use it because they are uncertain
of what it really does, since it doesn't map in a
straightforward way to the algorithm description provided
by Affy.  And there is no way of knowing how to call it
so that it performs calculations akin to the ones mentioned
in Affy's documentation.

Best,
Michal Blazejczyk
FlexArray Lead Developer
http://genomequebec.mcgill.ca/FlexArray/




> Hi Ingrid,
> We are working on updating the docs within the package - at the moment, the
> best source of information about Plier is at the Affymetrix website. The
> parameter names in the function should translate relatively easily to the
> Affy documentation.
> Regards,


> Crispin



> On 14/11/07 14:50, "Ingrid H. G. ?stensen"
> <Ingrid.H.G.Ostensen at rr-research.no> wrote:

>> Hi
>> 
>> Does it exist any documentation on how to use the plier package?
>> 
>> Regards,
>> Ingrid