[BioC] avereps function in limma (dealing with negative values in illumina)

[Prasad Siddavatam]

> 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