Dear affyPara package maintainers and BioC developer community,


The parallelizations of Affy preprocessing in the affyPara package provide
essential tools to handle large array collections.

Before starting to hack on this myself, I would like to ask if there are
workarounds in affyPara to obtain a preprocessed & normalized (but not
summarized) PM intensity matrix from CEL files? Alternatively, having an
access to virtual affybatch (i.e. keeping it in the nodes without 'rebuild')
would solve the problem. Is such functionality available?

I would need the probe-level values (for PM probes) after preprocessing and
normalization (but without probeset summarization step)  - in an ideal case
a probes x arrays matrix, and not necessarily other information from the
affybatch object. It seems that both background correction and normalization
can be done in affyPara by reading in the CEL files directly. However, the
output of these methods in itself an affybatch which will cause the memory
problems the package is trying to solve.

Thanks once more for relevant work.

with kind regards

Leo Lahti
Department of Information and Computer Science
Aalto University School of Science and Technology
Finland

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