This depends on what style manual you , your
publisher,  or your institution uses.  One common syle
(APA ) recommends this: 
http://library.osu.edu/sites/guides/apagd.php#sid  
--- "Vallejo, Roger" <Roger.Vallejo at ARS.USDA.GOV>
wrote:
> Dear All,
> How to cite the PDF user's guide for the LIMMA
> package?
> This is not about how to cite the LIMMA package.
> Roger
> 
> 
> Roger L. Vallejo, Ph.D.
> Computational Biologist & Geneticist
> U.S. Department of Agriculture, ARS
> National Center for Cool & Cold Water Aquaculture
> 11861 Leetown Road
> Kearneysville, WV 25430
> Voice:	(304) 724-8340 Ext. 2141
> Email:	roger.vallejo at ars.usda.gov