Hi Deepak,
I faced the same problem recently and have found a few routes out. If you've solved yours do inform me how you did it.
As said by Ben you could decimate the samples. Another way around is to re-configure your board for each set of channels. This also works when for some channels you want waveform data while for others it is scaled/binary data.
Best,
Gurdas
gurdas@qagetech.com
Gurdas Sandhu, Ph.D.
ORISE Research Fellow at US EPA