[BioC] Masking single Oligos in mas5

Jenny Drnevich drnevich at uiuc.edu
Thu Dec 1 17:37:39 CET 2005

See the three posts by Ariel Chernomoretz 
<ariel.chernomoretz at crchul.ulaval.ca> on 20-21 April, 2005. I've been using 
these codes to remove entire probe sets.

Thanks Ariel!!


At 10:06 AM 12/1/2005, Benjamin Otto wrote:
>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,
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch

Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu

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