To determine the stable housekeeping genes in your experiment you can use this excel-based tool using pair-wise correlations.

The first step in your qPCR gene expression analysis shoul be the test of your housekeeping (or reference) genes that usually are assumed that present a stable expression among samples, but could be affected by some experimental conditions (these reference genes can exhibit either up or down regulation).

This software is a free tool to determine the best standard genes to normalize your data. It allows you to test up to ten candidates, and combines them into an index. The index can be compared with further ten target genes to decide, whether they are differentially expressed under an applied treatment.

To download this software and read the description of  BestKeeper software - visit here.