[BioC] Background correction with just a few spots

[Wei Shi]

Dear January:

	The function neqc in limma package uses intensities from negative control probes to perform a normexp background correction, followed by quantile normalization and log2 transformation. For the details of this method, please see the paper:

http://nar.oxfordjournals.org/content/early/2010/10/06/nar.gkq871.abstract

	In brief, this method fits a normal+exponential convolution model to the data but use the negative control probe intensities to estimate the mean and standard deviation of background intensities.

	Let me know if you have any further questions.

Cheers,
Wei

On Nov 10, 2010, at 7:56 PM, January Weiner wrote:

> Dear all,
> 
> I have a set of "strange" microarrays (nylon membrane / radioactive
> labels). The raw data contains signals for the gene probes (a small
> microbial genome) and for a number of probes which constitute the
> background. There is no background signal directly in the data (like
> in regular microarray chips), and I would like to subtract background
> that is calculated from these few "background spots". Currently, I
> just subtract the average of the background spots from all the other
> spots.
> 
> In limma, what would be the most appropriate way to do it?
> 
> Cheers,
> j.
> 
> -- 
> -------- Dr. January Weiner 3 --------------------------------------
> Max Planck Institute for Infection Biology
> Charitéplatz 1
> D-10117 Berlin, Germany
> Web   : www.mpiib-berlin.mpg.de
> Tel     : +49-30-28460514
> 
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