Hi Prasad:

	I had a close look at one of the datasets: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?view=data&acc=GSM614020&id=15413&db=GeoDb_blob51 . The header information in this page is:

#ID_REF = 
#VALUE = Quantile, subtract background
#1690411024_A.Detection Pval = 

It looks like they performed quantile normalization to the data but also subtracted probe intensities by the background intensity. The negative values in the table seemed to result from the "subtract background" step. However, it is unclear how the data was analyzed at all. 

I would suggest you to contact the authors who generated these data. This might be the easiest and quickest way to get around this issue and get the data you want.

Hope this helps.

Cheers,
Wei
	
On Apr 8, 2011, at 11:25 AM, Prasad Siddavatam wrote:

>> Dear Prasad:
>> 
>>    I am not quite sure what your question is. But if you want to
>> normalize the raw data by yourself and you want use the control probes for
>> the normalization, then you might try limma neqc function which can infer
>> the intensities of negative control probes using regular probe intensities
>> and their detection p values. The neqc function will then perform a
>> normexp
>> background correction aided by negative controls followed by quantile
>> normalization and log2 transformation.
>> 
>>    Hope this helps.
>> 
>> Cheers,
>> Wei
>> 
> 
> 
> Thank you very much for Wei, Simon and Pan,
> 
> Well, the Problem is there are two files available at NCBI GEO. This is 
> the actual study GSE25001 but I want to use LIMMA package on their data.
> 
> I see both raw data and normalized data but can't find information for 
> probe.profile information and control probe profile to use LIMMA.  There are 
> zeros in raw data.
> 
> Appreciate your help,
> 
> Prasad
> 
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