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

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