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

Zhijin Wu zwu at stat.brown.edu
Thu Aug 27 15:20:49 CEST 2009


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



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