Fisher's exact test is a statistical significance test used in the analysis of contingency tables where sample sizes are small. It is named after its inventor, R. A. Fisher, and is one of a class of exact tests, so called because the significance of the deviation from a null hypothesis can be calculated exactly rather than by relying on a test statistic having a distribution that is approximately that of a known theoretical distribution. Since no freely available script existed which could perform Fisher's exact test batch wise, I developed one. I used this to calculate the significance of thousents of descritized measurements between two different cancer groups.

One of nine women will develop breast cancer in her life time. Of these cancers 90% are sporadic while 10% is due to inherited mutations. When inheriting mutated a BRCA1 gene, the lifetime risk for breast cancer increases up to 85%. Breast cancer cells accumulate mutations which lead to the instabillity of the chromosomes (packed DNA). Aberrations such as losses and gains of genomic material (DNA containing genes) will then accure. These aberrations can be used to recognize and classify breast tumors to different sugroups to optimize treatment regimens. 'BRCA1 classifier' is a program that can distinguish such a genomic profile of BRCA1-associated from sporadic breast tumors which is used in the Netherlands Cancer Institute as an additional diagnostic tool for unresolved breast cancer cases (still in research setting).

atCGH was developed for researchers at the Netherlands Cancer Institute (NKI). This program analyses and prosecces array-CGH data. CGH stands for Comparative Genomic Hybridization and is a technique used to investigate chromosomal instabillity, in for instance cancer. A microarray lets the user investigate thousents of different genomic locations simultaneously. atCGH processes and normalizes the raw values of these micro array data which then can be used in downstream analyses.