[BioC] vsn2 and print-tips

Hans-Ulrich Klein h.klein at uni-muenster.de
Tue Mar 4 17:38:53 CET 2008

Dear all,

I use the vsn2 method to normalize single-colour arrays with 48 
print-tips (25*26 oligos per print-tip). After normalization, the 
intensities of the 48 print-tips are in different ranges. The grid of 
the print-tips can be seen clearly on false color representations of the 
arrays' spatial distributions of feature intensities. However, scale and 
location of the intensities of a print-tip do not change across arrays.

The man page of vsn2 says:
"The data are returned on a glog scale to base 2. More precisely,
the transformed data are subject to the transformation
glog2(f(b)*x+a) + c, where glog2(u) = log2(u+sqrt(u*u+1)) =
asinh(u)/log(2) is called the generalised logarithm, a and b are
the fitted model parameters (see references), f is a parameter
transformation [4], and the overall constant offset c is computed
from b such that for large x the transformation approximately
corresponds to the log2 function."

May be there are not enough "large x" in some print-tips due to missing 
values in my data. I observed that reducing the number of oligos leads 
to even larger differences in the print-tip offsets. Are there 
parameters to take influence on the computation of c? Has someone else 
observed this problem? The older "vsn" function does not lead to 
different print-tip offsets.


 > sessionInfo()
R version 2.6.2 (2008-02-08)


attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods 
[8] base    

other attached packages:
[1] vsn_3.2.1            limma_2.12.0         affy_1.16.0        
[4] preprocessCore_1.0.0 affyio_1.6.1         Biobase_1.16.3     

loaded via a namespace (and not attached):
[1] grid_2.6.2      lattice_0.17-4  rcompgen_0.1-17

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