[amelia] 1)amelia across conditions, 2)function for pooling data

Good morning, I am using amelia II on mass spec data, in order to deal with missing values. I have two questions: 1) my experimental setup is as follows: the intensities of the same proteins were measured in ctrl, condition 1, condition2, condition3, condition4. This model implies that certain proteins might not be present at all in a certain condition, while being present in several other conditions. hence, I don not want amelia to impute these values. In other words, I want amelia to only impute WITHIN conditions. At least this is the way I though of this problem and I sub-devided the data frame into 5, according to conditions, and fed amelia each condition separately. Is this approach OK? 2) I perform m=10 imputations, and fit each imputed data set to a linear model, hence I get 10 slightly different outputs. In R, what is the best way to pool the results of m data sets? Thank you very much for your help, I appreciate it. Have a good New Years!! Regards, Elisa