[BioC] Agilent duplicate spots and multiple probes per gene

[Peder Worning]

Hi Nathan,

I answered a very similar question about duplicated spots on arrays last
Wednesday (May 6). You can find some code there. I recommend median of
duplicated spot instead of average. 

God luck

Peder

Best regards 

Exiqon A/S

 Peder Worning, Ph.D.

Senior Scientist, Biomarker Discovery


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Nathan S.
Watson-Haigh
Sent: Wednesday, May 13, 2009 2:51 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Agilent duplicate spots and multiple probes per gene

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I'm a bit confused/worried about duplicated spots on the Agilent bovine
array,
in particular how best to handle them in limma as I have technical rep
dye-swaps.

<code>
> #Get all non-control spots:
> genes.idx <- which(RG$genes$ControlType == 0)
> MA.none <- normalizeWithinArrays(RG[genes.idx,], method="none")
> table(table(MA.none$genes$ProbeUID))

    2     6
21465    10
</code>

So 21465 probes are duplicated twice and 10 probes are duplicated 6
times. Does
anyone have suggestions on how best to proceed given that I have
technical rep
dye-swaps?

Also, how do I best handle those genes with multiple different probes?
Simply
average?

Cheers,
Nathan

- --
- --------------------------------------------------------
Dr. Nathan S. Watson-Haigh
OCE Post Doctoral Fellow
CSIRO Livestock Industries
Queensland Bioscience Precinct
St Lucia, QLD 4067
Australia

Tel: +61 (0)7 3214 2922
Fax: +61 (0)7 3214 2900
Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html
- --------------------------------------------------------

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