[BioC] BioC normalisations for small array 2 colour data?

[Sean Davis]

On Thursday 07 September 2006 08:44, Dan Swan wrote:
> Hi,
>
> I have some data from a small specialised microarray - 200 genes, 1
> spiked control, 1 negative control.  This is 2 colour data, with dye
> swaps.  I was wondering what an appropriate normalisation for this
> scenario is within Bioconductor given that Lowess is unreliable for
> <1000 genes?

There is no "correct" answer here.  You will need to look at the data and 
determine what needs to be done.  Scatterplots, density plots/histograms, and 
M vs. A plots can help. 

If your genes were chosen because they were all thought to be differentially 
expressed, then any normalization method for two-color arrays will be 
inappropriate and you should probably think about single-channel 
normalization.  

Sean