A deal’s a deal, right?

Wrong. Not if you are a certain senior vice president for Affymetrix.

On Wednesday the Santa Clara provider of genetic analysis tools detailed the good-bye package it gave to Thane Kreiner. (Oh, by the way, his employment with the company ended July 27, something you might not have known had you not read this filing.)

Kreiner’s letter of agreement when he was first appointed to head up sales and marketing in April 2006 laid out the terms of his termination any time before an initial 18-month period. He would be entitled to the remainder of the salary he would have received through Oct. 2007, along with health coverage and vesting of his stock awards through the end of the period.

Kreiner had served 15 months and a week of the 18-month period when his employment was “terminated” July 27. By our calculations, he was due roughly $77,000 in residual salary along with health coverage and vesting rights through Oct. 20 under the terms of his signing agreement.

Instead, Affymetrix agreed to pay him $362,308, the salary he would have received through October 20, 2008 – an extra year – plus $117,000, of his annual target bonus along with an additional year of heath coverage and vesting of his stock awards.

But wait, there’s more. Kreiner’s was also guaranteed up to 12 months of job placement services worth $20,000, and “reasonable legal counsel fees incurred” in connection with the execution of the separation agreement, not to exceed $50,000.

Golden Parachute of the Day

The winner today is John D. Heaton, former President and Chief Executive Officer of Nanometrics. The company announced that Heaton had left on March 27. In a filing Tuesday, the company discussed his “termination.”

Nanometrics is based in Milpitas and makes scientific instruments. Its stock had fallen by about half during Heaton’s final year. Losses ballooned in 2006 to $22.1 million from $1.5 million in 2005.

As a parting gift, Heaton gets 12 months salary, which in 2005 was $364,400. And the company accelerated the vesting on 66,667 options. With the stock closing at $6.80 per share on Tuesday, that would make them worth $453,335.60.