sample from multiple pens When sampling from animals in different pens of the same farm, first, think about what your unit of replication is. This is not a trivial as it sounds (a pen with 20 animals in it is not necessarily n = 20!). A common mistake is to have all members of Group 1 in one pen, and all members of Group 2 in another. The unit of replication in this case would be pen not individual (i.e., one pen would constitute n = 1!). The reason this is important is because the variability within each pen will usually be lower than the variability between each pen. So, any effect that you observe might be an effect of pen, rather than an effect of your treatment.

One way to deal with this is to employ a phase design:

AB
ABA
ABAB

where 'A' is baseline and 'B' is your treatment (x).

These types of design are very useful as the allow you to return to baseline to ensure that any effects of treatment are not due to uncontrolled factors. Also, you can randomize the order of 'A' and 'B' between the different enclosures:

Week 1 Week 2
 Week 3
 Week 4
Pen 1
 A
 B
 A
 B
Pen 2
 B
 A
 B
 A

It is a good idea to plan to carry out at least one (preferably more than one) independent replication of the study.

Finally, don't forget that as you have not used random sampling (i.e., all of the animals have come from one farm) you cannot generalise your findings beyond this study! To do this, you would need to collect a random sample from the population.