Comput Methods Programs Biomed - Micro-Analyzer: automatic preprocessing of Affymetrix microarray data.


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A current trend in genomics is the investigation of the cell mechanism using different technologies, in order to explain the relationship among genes, molecular processes and diseases. For instance, the combined use of gene-expression arrays and genomic arrays has been demonstrated as an effective instrument in clinical practice. Consequently, in a single experiment different kind of microarrays may be used, resulting in the production of different types of binary data (images and textual raw data). The analysis of microarray data requires an initial preprocessing phase, that makes raw data suitable for use on existing analysis platforms, such as the TIGR M4 (TM4) Suite. An additional challenge to be faced by emerging data analysis platforms is the ability to treat in a combined way those different microarray formats coupled with clinical data. In fact, resulting integrated data may include both numerical and symbolic data (e.g. gene expression and SNPs regarding molecular data), as well as temporal data (e.g. the response to a drug, time to progression and survival rate), regarding clinical data. Raw data preprocessing is a crucial step in analysis but is often performed in a manual and error prone way using different software tools. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of different microarray data are needed. The paper presents Micro-Analyzer (Microarray Analyzer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix gene expression and SNP binary data. It represents the evolution of the ?-CS tool, extending the preprocessing to SNP arrays that were not allowed in ?-CS. The Micro-Analyzer is provided as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data (gene expression and SNPs) by invoking TM4 platform. It avoids: (i) the manual invocation of external tools (e.g. the Affymetrix Power Tools), (ii) the manual loading of preprocessing libraries, and (iii) the management of intermediate files, such as results and metadata. Micro-Analyzer users can directly manage Affymetrix binary data without worrying about locating and invoking the proper preprocessing tools and chip-specific libraries. Moreover, users of the Micro-Analyzer tool can load the preprocessed data directly into the well-known TM4 platform, extending in such a way also the TM4 capabilities. Consequently, Micro Analyzer offers the following advantages: (i) it reduces possible errors in the preprocessing and further analysis phases, e.g. due to the incorrect choice of parameters or due to the use of old libraries, (ii) it enables the combined and centralized pre-processing of different arrays, (iii) it may enhance the quality of further analysis by storing the workflow, i.e. information about the preprocessing steps, and (iv) finally Micro-Analzyer is freely available as a standalone application at the project web site

Resumo Limpo

current trend genom investig cell mechan use differ technolog order explain relationship among gene molecular process diseas instanc combin use geneexpress array genom array demonstr effect instrument clinic practic consequ singl experi differ kind microarray may use result product differ type binari data imag textual raw data analysi microarray data requir initi preprocess phase make raw data suitabl use exist analysi platform tigr m tm suit addit challeng face emerg data analysi platform abil treat combin way differ microarray format coupl clinic data fact result integr data may includ numer symbol data eg gene express snps regard molecular data well tempor data eg respons drug time progress surviv rate regard clinic data raw data preprocess crucial step analysi often perform manual error prone way use differ softwar tool thus novel platform independ possibl open sourc tool enabl semiautomat preprocess annot differ microarray data need paper present microanalyz microarray analyz crossplatform tool automat normal summar annot affymetrix gene express snp binari data repres evolut cs tool extend preprocess snp array allow cs microanalyz provid java standalon tool enabl user read preprocess analys binari microarray data gene express snps invok tm platform avoid manual invoc extern tool eg affymetrix power tool ii manual load preprocess librari iii manag intermedi file result metadata microanalyz user can direct manag affymetrix binari data without worri locat invok proper preprocess tool chipspecif librari moreov user microanalyz tool can load preprocess data direct wellknown tm platform extend way also tm capabl consequ micro analyz offer follow advantag reduc possibl error preprocess analysi phase eg due incorrect choic paramet due use old librari ii enabl combin central preprocess differ array iii may enhanc qualiti analysi store workflow ie inform preprocess step iv final microanalzy freeli avail standalon applic project web site httpsourceforgenetprojectsmicroanalyz

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