title: Goulphar: rapid access and expertise for standard two-color microarray normalization methods.
abstract: BACKGROUND
  Raw data normalization is a critical step in microarray data analysis because it directly affects data interpretation. Most of the normalization methods currently used are included in the R/BioConductor packages but it is often difficult to identify the most appropriate method. Furthermore, the use of R commands for functions and graphics can introduce mistakes that are difficult to trace. We present here a script written in R that provides a flexible means of access to and monitoring of data normalization for two-color microarrays. This script combines the power of BioConductor and R analysis functions and reduces the amount of R programming required.
  
  
  RESULTS
  Goulphar was developed in and runs using the R language and environment. It combines and extends functions found in BioConductor packages (limma and marray) to correct for dye biases and spatial artifacts. Goulphar provides a wide range of optional and customizable filters for excluding incorrect signals during the pre-processing step. It displays informative output plots, enabling the user to monitor the normalization process, and helps adapt the normalization method appropriately to the data. All these analyses and graphical outputs are presented in a single PDF report.
  
  
  CONCLUSIONS
  Goulphar provides simple, rapid access to the power of the R/BioConductor statistical analysis packages, with precise control and visualization of the results obtained. Complete documentation, examples and online forms for setting script parameters are available from http://transcriptome.ens.fr/goulphar/.
authors.affiliation: IFR36, Plate-forme Transcriptome, Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris cedex05, France. slemoine@biologie.ens.fr
authors.forename: Sophie
authors.initials: S
authors.lastname: Lemoine
authors.forename: Florence
authors.initials: F
authors.lastname: Combes
authors.forename: Nicolas
authors.initials: N
authors.lastname: Servant
authors.forename: Stéphane
authors.initials: S
authors.lastname: Le Crom
mesh_terms: D000465:Algorithms; D002138:Calibration; D005103:Expert Systems; D017404:In Situ Hybridization, Fluorescence / Q000379:methods* / Q000592:standards; D036641:Microscopy, Fluorescence, Multiphoton / Q000379:methods* / Q000592:standards; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012984:Software; D014584:User-Computer Interface