Pipeline for macro- and microarray analyses

The pipeline for macro- and microarray analyses (PMmA) is a set of scripts with a web interface developed to analyze DNA array data generated by array image quantification software. PMmA is designed for use with single- or double-color array data and to work as a pipeline in five classes (data format, normalization, data analysis, clustering, and array maps). It can also be used as a plugin in the BioArray Software Environment, an open-source database for array analysis, or used in a local version of the web service. All scripts in PMmA were developed in the PERL programming language and statistical analysis functions were implemented in the R statistical language. Consequently, our package is a platform-independent software. Our algorithms can correctly select almost 90% of the differentially expressed genes, showing a superior performance compared to other methods of analysis. The pipeline software has been applied to 1536 expressed sequence tags macroarray public data of sugarcane exposed to cold for 3 to 48 h. PMmA identified thirty cold-responsive genes previously unidentified in this public dataset. Fourteen genes were up-regulated, two had a variable expression and the other fourteen were down-regulated in the treatments. These new findings certainly were a consequence of using a superior statistical analysis approach, since the original study did not take into account the dependence of data variability on the average signal intensity of each gene. The web interface, supplementary information, and the package source code are available, free, to non-commercial users at http://ipe.cbmeg.unicamp.br/pub/PMmA.

Validity of the Brazilian version of WHOQOL-BREF in depressed patients using Rasch modelling

OBJECTIVE: To assess the validity of the Brazilian version of the World Health Organization Quality of Life Instrument - Abbreviated version (WHOQOL-BREF) in adults with major depression, using Rasch modelling. METHODS: Study analyzing data from the baseline sample of the Longitudinal Investigation of Depression Outcomes in Brazil, including a total of 208 patients with major depression recruited in a primary care service in Porto Alegre (Southern Brazil), in 1999. The Center for Epidemiological Studies Depression Scale was used to assess intensity of depression; the WHOQOL-BREF to assess generic quality of life; and the Composite International Diagnostic Interview version 2.1 for the diagnosis of depression. RESULTS: In the Rasch analysis, the four domains of WHOQOL-BREF showed appropriate fit to this model. Some items needed adjustments: four items were rescored (pain, finances, services, and transport); two items (work and activity) were identified as having dependency of responses, and one item was deleted (sleep) due to multidimensionality. CONCLUSIONS: The validation of the WHOQOL-BREF Brazilian version using Rasch analysis complements previous validation studies, evidencing the robustness of this instrument as a generic cross-cultural quality of life measure.