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What is Goulphar for?

Goulphar is a tool to normalize microarray data. It proposes various normalization methods:
  • Print-tip lowess
  • Global lowess
  • Global median
  • Global Lowess followed by print-tip median
  • Print-tip median
Before normalization, you can perform filters on your data such as removing flags, small spots and saturating spots. It builds graphical outputs so that you can check your data before and after normalization. Its inputs can be either a GenePix (gpr file) or a Spot (spot file) output file and a tabulated text file that contains the normalization parameters you want (See "Make a parameter file"). When work is completed, you get your normalized data in a tabulated text file and a pdf report with graphical output (or separate png or jpeg files).
To use Goulphar (See "Download Goulphar"), you have to install R and a few bioconductor packages on your computer (See "How to install R and bioconductor package"). Goulphar is a free R script, distributed under the terms of the GNU General Public License.

Graphical output examples

A word about R

Goulphar is written in R, a language that enable statistical and graphical programming. It is very close to the language S+. R is freely available for Windows, MacOs and Linux. Source codes and packages are available on the R project site. The role of R in biology is more and more important, packages are developped to fit biological questions, especially in large scale biology. A R project called bioconductor is fully dedicated to bioarrays. It bundles a large set of packages to help in normalizing and analyzing bioarray data.

  Goulphar is a lighthouse located in Belle-ile, a southern brittany island. It was built from 1824 to 1836.

Last page update: February 12th, 2007 - 16:17 | For any questions or comments send an e-mail to the Goulphar team