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

Rullmann, J.A.C. (Ton) ton.rullmann at spcorp.com
Fri Aug 28 14:02:06 CEST 2009


Hi Jean,
>From your answer I get the idea that only probes with (very) low
intensity should be affected. However, I find differences for probes at
all levels of intensity (2log intensity after gcrma between 2 and 15).

In the HGU133PLUS2 example given in my first email the difference
between the BioC 2.0 and 2.4 results from gcrma are not that large: over
48 arrays the ratio new/old of the log-intensity values is 1.001 +/-
0.020, and the ratio of the intensity values is 1.007 +/- 0.090.
 
In another set of arrays, of the RGU34A type, the difference between the
BioC 2.0 and 2.4 results from gcrma is much larger: over 8 arrays the
ratio new/old of the log-intensity values is 1.05 +/- 0.16, and the
ratio of the intensity values is 1.4 +/- 1.3!
For ~5 % of the cases the new intensity value is more than four-fold
different than the old value. The effects are partially conserved
between arrays, but identification of regulated genes still gives a list
that is 10% different than the previously obtained set, using the same
selection criteria.
Differences already occur after bg.adjust.gcrma. I verified by dumping
the data from the R sessions that the probe files that were used
(rgu34aprobe_2.4.0 and rgu34aprobe_2.2.0) are identical.

Does anyone else have similar experiences? What is the explanation?

Thanks for your help. 

Ton Rullmann
T: +31 412 661423
ton.rullmann at spcorp.com


-----Original Message-----
From: Zhijin Wu [mailto:zwu at stat.brown.edu] 
Sent: Thursday, 27 August, 2009 15:21
To: Rullmann, J.A.C. (Ton)
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Different gcrma output values after upgrade BioC 2.0
-> 2.4

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
> 
> 
> 
> This message and any attachments are solely for the intended
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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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