[BioC] Different gcrma output values after upgrade BioC 2.0 -> 2.4

[Zhijin Wu]

The most recent change is on probes with intensity at lower bounds. 
These use to go through the same adjustment for specific binding 
(GSB.adjust), but are no longer adjusted b/c they are believed to bear 
no signal.

-- thanks to Wei Keat Lim and colleagues who brought it up in their 
paper "Comparative analysis of microarray normalization procedures:
effects on reverse engineering gene networks"
Lim et al, Bioinformatics 2007 Vol23(13):i282

Rullmann, J.A.C. (Ton) wrote:
> Hi,
> We upgraded from BioC 2.0 to BioC 2.4. Now I note that log-intensities
> computed by gcrma differ from the values I got previously, for the same
> input.
> For example, for one array the mean ratio of old vs new log-intensities
> is 0.9996 with an sd of 0.0187.
> For a second array, analyzed in the same set, the mean and sd values are
> 0.9991 and 0.0197.
> This implies there are dozens of probe sets for which the computed
> log-intensity changes by ~ 10%.
> 
> Is this "expected behaviour", that is: has the gcrma algorithm changed?
> 
> Thanks,
> 
> Ton Rullmann
> Senior Research Scientist
> Project Leader Systems Biology
> Dept. Molecular Design and Informatics
> Schering-Plough
> RK 2309
> PO Box 20
> 5340 BH Oss, The Netherlands
> www.schering-plough.com
> 
> 
> 
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-- 
------------------------------------
Zhijin (Jean) Wu
Assistant Professor of Biostatistics
Brown University, Box G-S121
Providence, RI  02912

Tel: 401 863 1230
Fax: 401 863 9182
http://www.stat.brown.edu/zwu