[BioC] Normalization with cDNA microarray Control Spot / limma

[Gordon Smyth]

At 11:14 PM 27/07/2004, Sek Won Kong,M.D wrote:
>Hi,
>
>We made custom cDNA microarray, and put 20 control spot out of 360 total
>features in a single slide.
>
>I'd like to know whether limma has a normalization function that uses
>control spots. If yes, how to define control spots in limma? If no, is there
>any other package that can handle normalization with control spots?

How one would use control spots in normalization depends on what sort of 
"control" the spots are designed to give. What sort of control spots are 
they? Positive? Negative? Non-differentially expressed? Ratio? Range of 
intensities?

Look at the documentation for ?controlStatus and look through the various 
postings to this maillist which use controlStatus to define control spots.

Gordon

>I want to make MvA plot with control spots on straight line.
>
>Thank you for the helps in advance.
>
>-Sek Won