[BioC] R-2.2 and BioConductor 1.7: changes in GC-RMA and fitPLMprocedures

Groot, Philip de philip.degroot at wur.nl
Tue Oct 18 15:23:37 CEST 2005


Just a small additional note. I just found out that both commands:
bg.adjust.gcrma() and bg.correct.gcrma() return exactly the same
results, thus solving my problem. I was confused by two different
function calls that, in the end, do the same thing. I apologize for any


Dr. Philip de Groot
Wageningen University

-----Original Message-----
From: Groot, Philip de 
Sent: Tuesday, October 18, 2005 10:16 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] R-2.2 and BioConductor 1.7: changes in GC-RMA and



I submit this message to the mailing list because I think that more
people encounter the same problem. In general, when performing quality
control calculations, performing fitPLM calculations (affyPLM package)
is a good idea. Normalizing your data is also a good idea, so (in our
situation) the same calculations are performed two times: fitPLM
executes an GC-RMA background correction and the same thing is done when
applying the GC-RMA normalization. This was for me a reason to combine
both calculations in a separate script in BioC 1.6, in which the GC-RMA
background correction is performed, used as input for the fitPLM
procedure, and the further normalization steps are executed afterwards
(this required digging in both scripts and perform the separate required
steps in a new script).


Unfortunately, in BioC 1.7 things has changed significantly in such a
way that it is more difficult to do the above things: all GC-RMA
calculations (except the summarization) are performed in
"bg.adjust.gcrma" while the fitPLM GC-RMA background correction is
performed in "bg.correct.gcrma" (without an option to pass the
previously calculated affinities to this function and to get the
in-between GC-RMA values back).


So, my question (request) is straightforward: are people working on a
better integration of these two scripts, so that the end result of
fitPLM can be used for the further GC-RMA normalization procedure? This
is not only more efficient, but also saves a considerable amount of
computation time!


Kind regards,


Dr. Philip de Groot

Wageningen University

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