[BioC] dealing with negative values in illumina

[Wei Shi]

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


On Mar 23, 2011, at 4:28 PM, Prasad Siddavatam wrote:

> 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
> 
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