Local disk not recognized

While online I received two pop ups that seemed to be typical of malware of some sort.
Both were in the same instance, the first told me that my system was at risk of intrusion and I should buy and run some software to protect it. I closed that window and another opened saying that some program ( I forget the name) was going to run and asked my permission. I closed that window after a couple attempts at clicking the X.
Since then my laptop doesn't recognize the partition that creates the largest storage area on my hard drive.
Multiple virus scans have come back with nothing.
I've heard that a virus that deletes a partition is an urban legend, but what then could be the problem.
Any help is greatly appreciated.

Try running the scans in safe mode? Might want to try one of those online scanners as well. (F-secure?) If you need the data you might be able to use Partition magic or some other such program to restore the partition.