Question: affyPara: background correction & normalization only?
9.6 years ago by
L L • 30
L L • 30 wrote:
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 [[alternative HTML version deleted]]
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