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1.  EMA - A R package for Easy Microarray data analysis 
BMC Research Notes  2010;3:277.
Background
The increasing number of methodologies and tools currently available to analyse gene expression microarray data can be confusing for non specialist users.
Findings
Based on the experience of biostatisticians of Institut Curie, we propose both a clear analysis strategy and a selection of tools to investigate microarray gene expression data. The most usual and relevant existing R functions were discussed, validated and gathered in an easy-to-use R package (EMA) devoted to gene expression microarray analysis. These functions were improved for ease of use, enhanced visualisation and better interpretation of results.
Conclusions
Strategy and tools proposed in the EMA R package could provide a useful starting point for many microarrays users. EMA is part of Comprehensive R Archive Network and is freely available at http://bioinfo.curie.fr/projects/ema/.
doi:10.1186/1756-0500-3-277
PMCID: PMC2987873  PMID: 21047405
2.  Model selection in the reconstruction of regulatory networks from time-series data 
BMC Research Notes  2009;2:68.
Background
A widely used approach to reconstruct regulatory networks from time-series data is based on the first-order, linear ordinary differential equations. This approach is justified if it is applied to system relaxations after weak perturbations. However, weak perturbations may not be informative enough to reveal network structures. Other approaches are based on specific models of gene regulation and therefore are of limited applicability.
Findings
We have developed a generalized approach for the reconstruction of regulatory networks from time-series data. This approach uses elements of control theory and the state-space formalism to approximate interactions between two observable nodes (e.g. measured genes). This leads to a reconstruction model formulated in terms of integral equations with flexible kernel functions. We propose a library of kernel functions that can be used for the first insights into network structures.
Conclusion
We have found that the appropriate kernel function significantly increases the accuracy of network reconstruction. The best kernel can be selected using prior information on a few nodes' interactions. We have shown that it may be already possible to select models ensuring reasonable performance even with as small as two known interactions. The developed approaches have been tested with simulated and experimental data.
doi:10.1186/1756-0500-2-68
PMCID: PMC2688516  PMID: 19416509
3.  Advanced spot quality analysis in two-colour microarray experiments 
BMC Research Notes  2008;1:80.
Background
Image analysis of microarrays and, in particular, spot quantification and spot quality control, is one of the most important steps in statistical analysis of microarray data. Recent methods of spot quality control are still in early age of development, often leading to underestimation of true positive microarray features and, consequently, to loss of important biological information. Therefore, improving and standardizing the statistical approaches of spot quality control are essential to facilitate the overall analysis of microarray data and subsequent extraction of biological information.
Findings
We evaluated the performance of two image analysis packages MAIA and GenePix (GP) using two complementary experimental approaches with a focus on the statistical analysis of spot quality factors. First, we developed control microarrays with a priori known fluorescence ratios to verify the accuracy and precision of the ratio estimation of signal intensities. Next, we developed advanced semi-automatic protocols of spot quality evaluation in MAIA and GP and compared their performance with available facilities of spot quantitative filtering in GP. We evaluated these algorithms for standardised spot quality analysis in a whole-genome microarray experiment assessing well-characterised transcriptional modifications induced by the transcription regulator SNAI1. Using a set of RT-PCR or qRT-PCR validated microarray data, we found that the semi-automatic protocol of spot quality control we developed with MAIA allowed recovering approximately 13% more spots and 38% more differentially expressed genes (at FDR = 5%) than GP with default spot filtering conditions.
Conclusion
Careful control of spot quality characteristics with advanced spot quality evaluation can significantly increase the amount of confident and accurate data resulting in more meaningful biological conclusions.
doi:10.1186/1756-0500-1-80
PMCID: PMC2556690  PMID: 18798985

Results 1-3 (3)