remove batch effect of SILAC protein data

Hello,

I have SILAC protein data which comes from three different days and want to remove batch effect of these data,

1. knn function of impute package to impute missing expression values.

2. na.omit to delete all the NA value.

None of them is work.

Is there any methods that can remove batch effect of this kind SILAC protein data?

Thank you in advance for any suggestion!

Best,

Yue