Sboner, A. and Romanel, A. and Malossini, A. and Ciocchetta, F. and Demichelis, F. and Azzini, I. and Blanzieri, E. and Dell'Anna, R. (2005) Simple methods for peak and valley detection in time series microarray data. UNSPECIFIED. (Unpublished)
Abstract
Given a set of gene expression time series obtained by a microarray experiment, this work proposes a novel quality control procedure, which exploits some analytical methods enabling the identification of genes which spike expressions within narrow time-windows and over a chosen amplitude threshold. The procedure automatically provides a list of genes and time points in which abrupt variations have been detected. The quality control has to be performed by a biologist, who assesses those spikes as bearing biology relevance or being artifacts. In the latter case spikes have to be substituted by a smoothing procedure. In particular, we focused on transcriptome of Plasmodium falciparum Intraerythrocytic Developmental Cycle. Assuming that spikes detected in this set have been labeled as artifacts by a biologist, in the second part of this paper we discuss the effects of smoothing on subsequent different types of analyses.
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