[BioC] dealing with negative values in illumina

[Prasad Siddavatam]

Dear List,

I am reprocessing a previously processed dataset from NCBI GEO. This is a 
Illumina microarray chip. The data provided at GEO is either normalized with 
negative probe values or unnormalized data without control spot information. 

If I avoid the probes with the negative values (can't transfer to logs) that 
leaves only 9500 out of 22000 probes?

Can anybody please suggest how to approach this problem? 

Appreciate your help

Prasad