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

[Gordon Smyth]

Dear Dan,

At 08:00 PM 8/09/2006, bioconductor-request at stat.math.ethz.ch wrote:
>Date: Thu, 7 Sep 2006 13:44:35 +0100
>From: "Dan Swan" <bioinformatics.lists at gmail.com>
>Subject: [BioC] BioC normalisations for small array 2 colour data?
>To: bioconductor at stat.math.ethz.ch
>
>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?

Are you quoting someone when you say that lowess is unreliable for 
<1000 genes? Who? Print-tip loess normalization is routinely applied 
to arrays with around 200 genes in each print-tip group so 200 genes 
is, far from being unusual, pretty much typical for loess normalization.

The real problem with a specialised microarray is the fact that the 
genes are not randomly chosen, indeed they are typically chosen 
because of their likelihood to be differentially expressed. Hence you 
may be in a situation where the majority of genes may be 
differentially expressed. If that is your case then, in my opinion, 
normalization control probes need to be designed into the array in 
the first place to produce reliable results.

Best wishes
Gordon

>Any pointers would be gratefully recieved.
>
>thanks,
>
>Dan
>
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