[BioC] Background correction with just a few spots

[Wolfgang Huber]

January,

if you're looking for a local background correction, there is a function 
in cellHTS2 that could be adapted to doing this:
   cellHTS2::spatialNormalization
It fits a local-regression surface based on the values of 'control 
spots' and subtracts that from the other ('sample') values. You'd either 
have to stuff your data into a cellHTS object (which is essentially an 
NChannelSet) or modify the function to not use class-specific 
slots/accessors but your primitive data structures.

	Best wishes
	Wolfgang




Il Nov/10/10 9:56 AM, January Weiner ha scritto:
> 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.
>