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.

Simple methods for peak and valley detection in time series microarray data / Sboner, A.; Romanel, A.; Malossini, A.; Ciocchetta, F.; Demichelis, F.; Azzini, I.; Blanzieri, E.; Dell'Anna, R.. - ELETTRONICO. - (2005), pp. 1-28.

Simple methods for peak and valley detection in time series microarray data

Sboner, A.;Romanel, A.;Malossini, A.;Ciocchetta, F.;Demichelis, F.;Blanzieri, E.;
2005-01-01

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.
2005
Trento
Università degli Studi di Trento - Dipartimento di Informatica e Telecomunicazioni
Simple methods for peak and valley detection in time series microarray data / Sboner, A.; Romanel, A.; Malossini, A.; Ciocchetta, F.; Demichelis, F.; Azzini, I.; Blanzieri, E.; Dell'Anna, R.. - ELETTRONICO. - (2005), pp. 1-28.
Sboner, A.; Romanel, A.; Malossini, A.; Ciocchetta, F.; Demichelis, F.; Azzini, I.; Blanzieri, E.; Dell'Anna, R.
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11572/357878
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