Entering edit mode
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.
Regards,
Hans-Ulrich
> sessionInfo()
R version 2.6.2 (2008-02-08)
x86_64-pc-linux-gnu
locale:
C
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