[BioC] microRNA microarray analysis

[Philipp Pagel]

> I am analyzing two color microarrays with limma but I am getting blank
> and empty spots as differentially expressed genes in topTable. I have
> made spot files but can't get get rid of them. 

You can use logical subsetting of your MA or RG object. E.g.  you could
use something like

RG = RG$genes$Status = controlStatus(spottypes, RG)
RGnoblanks = RG[!(RG$gene$Status %in% c('blank','empty')), ]

The only catch with this is that somehow the color attribute seems to
get lost in the process, resulting in a surprise the next time you use
plotMA(). But you can fix this by re-doing the controlStatus step. (BTW:
does anybody here know why the color attribute is dropped?)

The other side of the story is, that blank spots should not appear to be
differntially expressen in the first place...

cu
	Philipp

-- 
Dr. Philipp Pagel                              Tel.  +49-8161-71 2131
Lehrstuhl für Genomorientierte Bioinformatik   Fax.  +49-8161-71 2186
Technische Universität München
Wissenschaftszentrum Weihenstephan
85350 Freising, Germany

 and

Institut für Bioinformatik / MIPS
GSF - Forschungszentrum für Umwelt und Gesundheit
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85764 Neuherberg, Germany
http://mips.gsf.de/staff/pagel