Training for dog barking

Question
Our cockapoo is 4 months old and we got her 3 weeks ago. She is in a large pen alone for most of the day, but we leave plenty of toys, water, food, and we take her out for walks in mornings and evenings and play with her to release energy.  I started keeping her in one room of the house (baby gated) recently, but she barks and whines continually everytime I leave the room, sometimes for a few minutes, sometimes up to 15.  

She does not bark or whine for more than 2 minutes in the mornings when I leave for work as I think she is used to it.

I tried ignoring it, but that hasn't changed her barking. How can we train her to stop barking every time we leave the room/are not around her?

Thanks so much for your help.

Answer
Your puppy is way too young to be left alone in a room, unless there is absolutely nothing in it but her and her "stuff". Puppies will chew on anything. Personally, I would put her back in the pen as that is what she is used to. When you are home, she should be out with you, as being confined will teach her nothing at all. She is at an age when her little brain is like a sponge, soaking up everything it can... both good and bad. Start molding her into the dog of your dreams.

Get her into obedience classes and start working with her every day. Also, start practicing "Nothing in Life is Free" with her; everyone in the family should be doing this. http://k9deb.com/nilif.htm

When she is confined, she should be ignored (unless she sounds like she needs to potty). She may have a bit of separation anxiety, and you do not want to encourage that. Always leave a radio on for her when you leave the house.
http://www.ygrr.org/doginfo/behavior-anxiety.html
http://www.marvistavet.com/html/body_separation_anxiety.html