[BioC] Duplicated spots in limmaGUI

[Gordon K Smyth]

Dear Wonjong,

> Date: Wed, 18 Apr 2007 17:46:29 -0700
> From: "Wonjong Moon" <wonjong.moon at sbri.org>
> Subject: [BioC] Duplicated spots in limmaGUI
> To: <bioconductor at stat.math.ethz.ch>
>
> Our slide design had some spots were duplicated and some were not.
> I am using limmaGUI,

The duplicated spot method in limmaGUI is not applicable if not all probes are duplicated.  The
recommended procedure is that you simply treat the duplicates as independent probes.

> but duplicated spots were recognized by space
> between spots.

I don't know what you mean by this.

> How can I handle the spots that were not duplicated?
> Should add flags in spottype file and exclude those?

No.  Well, I can imagine some special arrays with a small number of non-duplicate control spots,
for which the non-duplicated could be removed.  But this would only be sensible for special
arrays, and it involves some checking that you're not likely to do if you're using limmaGUI rather
than the command-line package.

> Is there any way to combine duplicated spots by ID or name in Limma?

No.

Best wishes
Gordon

> Thank you.
>
> Wonjong.
> Bioinformatician
> SBRI.