[BioC] dealing with missing values in microarray data set

[Amit Kumar]

Hi! All,

I am trying to analyze very large microarray data sets with 550
arrays. But there are lots of missing values (NA) in the data set
which is making my life difficult.
So I need to get rid of those NAs in the data. I do not want to
impute. Also, I can not remove those rows containing NAs as almost
each row have it.
Is it a good idea to replace NAs with zero in the data set. If yes,
why? and if not, why not? Your suggestion will be invaluable.

cheers!
Amit