Pet Rat Nervous

Question
I hold my two pet rats every day and they are very social and love to play. Jem
is normally at the top of the cage and loves to come out. Last night I was
holding them with a friend and they both seemed a bit nervous. They are
used to this friend and have been handled by her often. Pheobe seemed just a
little nervous but Jem was frozen. She then jumped out of my hands and off
of my bed very quickly and hit in some clothes. I was able to pick her up and
put her in her cage. Today my rat Pheobe is acting normal but Jem runs to the
bottom of the cage when I open it. She accepts treats through the bars but if
the cage is open she looks very frightened. Why might this be happening?
They are about 3 months old and I have had them for two months. She is
normally very social and rarely shy. I am a bit concerned. How should I
proceed? Should I try to hold her even if she does not want to come out?

Answer
Rats are strange sometimes. It is so hard to know what they are thinking  and we have to try to understand how they do think. They are "wired" to not trust anything outside their own species and for darn good reason: They are a source of food for many other species of animals and also are a target for extermination by some members of the human race. I would be scared too. However, if handled at birth and raised by human hands, they usually are not half as timid. Many people think that if they buy rats from a breeder that the rats are bred to be more outgoing but it has nothing to do with genetics. Even the most friendly rat can produce shy babies if they are not hand held from birth by humans.
Female rats are less trusting than males because they have to protect their young. Males are a bit more trusting but ready to fight at any given moment, usually fleeing first but will usually not back down from a challenge once he is at his limit. Much to our confusion, sometimes our most outgoing rats can regress, so to speak, and all of a sudden it seems something spooks them and off they go, fleeing back to safety and being cautious for a day or two until they forget what it was that spooked them. Not that rats are forgetful but they learn by repetition and if the same incident is not repeated again and again they eventually forget about it.  I have had rats that were 2 and even 3 years old, totally used to their room they play in and everything in and out of their cage, but one time one of my older girls freaked out, ran back to the cage and actually had herself so upset she was trembling. At first I had no clue what was going on, but quickly realized I had brought in something that she never saw before and did not understand what it was
and here, I had brought in a  big orange gift  bag that was from a birthday present. I thought they would like playing in it and turns out the bold colors really freaked her out.  She would come to the front of the cage and soon as she saw it was still there, she would scram back to hide in her igloo. I removed the bag and she remembered it was there for the rest of the day and must have thought that it was hiding and waiting for her.  LOL  She still wouldnt come out. Finally without seeing it she forgot about.  
I have all sorts of stories like that, to,

You may never know what spooked your girl but she will get over it   in time.  I would not force her out but just put your hand in the cage and let her get used to you but dont force her out or to be held. If things persist you can refer to my trust training page on  my website but I doubt she will stay like this too long.     

Info on training shy or biting rats:
http://www.freewebs.com/crittercity/trainingshyorbitingrats.htm