[BioC] Masking single Oligos in mas5

Benjamin Otto b.otto at uke.uni-hamburg.de
Thu Dec 1 17:06:59 CET 2005


I have been searching for nearly two days for a solution to the following
problem without finding satisfactory answers:

I am working on the analysis of a HG-U133_Plus2 Chip. Can I mask for certain
probesets single Oligos such that the expression, p and fold change values
are calculated based on the remaining oligos?

A better description of my problem and the background. We are handling a
cross-species experiment having hybradized rna from tupaia on the human
chip. This resulted in fairly low expression signals. If we just forget
about all the other putative problems in analysing the result I think it
seems reasonable to say, that in many cases only some of the probeset oligos
will have hybridized satisfyingly. So the idea is masking some of the oligos
by some criteria and calculate the results only based upon subsets of the
probesets. The problem is: If I set even only one single oligo to NA, the
values calculated for the corresponding probeset won't be calculated but set
to NA. Most of the threads I found concerning the masking problem handle the
question of an autpmated or corrected form of masking. But there seems to be
no available information about our case. Has anyone done something like that
before? I'm sure there will have to be some manual programing. But the major
question is: Does anybody see a possibility to mask the single oligos on a
top level like fixing the affybatch structure? Or do I have to change every
single function to treat NA values in the correct form?

thanks for your help,

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