Goulphar: rapid access and expertise for standard two-color microarray normalization methods

摘要: Raw data normalization is a critical step in microarray analysis because it directly affects interpretation. Most of the methods currently used are included R/BioConductor packages but often difficult to identify most appropriate method. Furthermore, use R commands for functions and graphics can introduce mistakes that trace. We present here script written provides flexible means access monitoring two-color microarrays. This combines power BioConductor reduces amount programming required. Goulphar was developed runs using language environment. It extends found (limma marray) correct dye biases spatial artifacts. wide range optional customizable filters excluding incorrect signals during pre-processing step. displays informative output plots, enabling user monitor process, helps adapt method appropriately data. All these analyses graphical outputs presented single PDF report. simple, rapid statistical packages, with precise control visualization results obtained. Complete documentation, examples online forms setting parameters available from http://transcriptome.ens.fr/goulphar/ .