Dear Rahmi,
Maybe you can make a composite (average cases) with netcdf operators like NCO or CDO.
I mean you can select the cases of any MJO phase and make a average. In cdo you could you operator -seltime to select the events.
Further, for significance level of your composite you should calculate the effective number (equivalent) of your sample, Because could be autocorrelation in the data, then the size of your sample could be smaller. An estimation of the sample size could be done with
http://clivac.geog.ucsb.edu/wp-content/uploads/dependence_files_image006.gif
where n is the size of sample, p1 is autocorrelation with lag-1 and n' is the effective number of independents events for composite.
You will use the n' for estimate the degrees of freedom (v), you could be and look up the t-student table to find the critical t-value.
I hope that helps,