[BioC] Masking single Oligos in mas5

[Ariel Chernomoretz]

Hi Benjamin,

Some time ago I wrote a couple of functions that modified
the cdf environments in order to remove bad probes from the affy analysis

You could check:

http://files.protsuggest.org/biocond/html/7350.html
http://files.protsuggest.org/biocond/html/7366.html
http://files.protsuggest.org/biocond/html/7367.html


hope that helps.

ariel./


On December 1, 2005 11:06 am, Benjamin Otto wrote:
> Hi,
>
> 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,
> Benjamin
>
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