[BioC] Agilent duplicate spots and multiple probes per gene

[Nathan S. Watson-Haigh]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

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
- --------------------------------------------------------

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.9 (MingW32)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iEYEARECAAYFAkoKGXkACgkQ9gTv6QYzVL4RyACeNQUXJABLApt0qF8fU6Yn90On
QY4AoJ+rYzYa8MGgmMt3mzzsBZ68+k8m
=1+Hx
-----END PGP SIGNATURE-----