A p p l i e d     B i o i n f o r m a t i c s





R e s e a r c h

T o o l s

P e o p l e

L i n k s
























T o o l s

This set of integrated tools have been developed in IFOM to facilitate the analysis of large amounts of Affymetrix ® GeneChip ™ expression data.

:: CHPReader

CHPReader reads *.CHP files saved in text format and performs preprocessing of the data. The user has the possibility to filter the data at this stage using a number of parameters (see below).


:: GenePicker

CHPReader output files can be loaded into GenePicker. GenePicker allows the user to set up analysis schemes and to search the data for regulated genes using t-test, ANOVA and a heuristic procedure called Change - Fold Change analysis.


:: CHPinfo

GenePicker generates a list of genes that are regulated with high confidence. CHPinfo allows retrieving up-to-date annotations for these genes. The annotations are based on the latest Unigene and LocusLink releases (currently available for human and mouse).


:: Samples

E2F samples
A set of samples can be downloaded to have an example of an analysis performed with these tools


Affymetrix Latin Square Data U133
Results of the analysis performed using GenePicker on U133 Latin Square Dataset.







Created by Giacomo Finocchiaro