Choice Impact of Soft Analysis Tools in Genes Selec- tion O.Kaissi 1 , A.Moussa 1 , B. Vannier 2 and A.Ghacham 1 1 LTI Laboratory, ENSA, University Abdelmalek Essaadi ,Morocco 2 IPBC, University of Poitiers, France amoussa@uae.ac.ma Abstract. Motivation: In the analysis of experiments that involves the high density of oli- gonucleotide chips, it is important to generate list of genes or ‘targets’ from the genomewide data set that contains a lot of information. Gene selection is a pro- cess that seeks to identify the most significant genes which reveal large expres- sion changes between the baseline experiments and the conditions. Even though, several algortithms like T-test and other derived statistical algorithms were used for that selection process, the suitable Pvalue Cutoff remains difficult to choose. Therefore, one solution consists of using a False Discovery Rate (FDR) control. The Significance Analysis of Microarray (SAM) and the T-test Benjamini & Hochberg (BH) algorithms have been successfully used in such way. However, the reproductivity of results and their impact on the genes and/or experiments classification, while using different soft tools remain a sub- ject of discussion. Method: we use two Affymetrix data sets, when we look for identifying list of genes under SAM and T-test-BH algorithms with FDR control runing under R/Bioconductor project and Bioinformtics ToolBox of Mathworks. Results: The list of selected genes changes significantly when using the two al- gorithms under both R/Bioconductor project and Bioinformtics ToolBox of Mathworks. By means of data provided from publicly databases, we illustrate, that the permutation process of the multiple statistical T-test (SAM and BH) may affect results of selection process. Moreover, list of genes using the two Soft is affected by the choice of the Pvalue-CutOff for identifyng true differen- tial expressed genes. According to this work, we present some results clarifying sensitivity and efficiency of used soft and its influence in gene selection pro- cess. Hierarchical classification of selected genes and corresponding experienc- es confirm the influence of both methods and tools on the outcome of gene ex- pression data analysis. 1 Introduction The preparation of manuscripts which are to be reproduced by photo-offset requires special care. Papers submitted in a technically unsuitable form will be returned for retyping, or canceled if the volume cannot otherwise be finished on time. The technology of DNA microarrays witnesses an exceptional growth and attracts a tremendous advantage in the scientific community. This interest lies in its efficiency; speed of obtaining results, and in its ability to study simultaneously the expression of IWBBIO 2013. Proceedings Granada, 18-20 March, 2013 185