[BioC] Agilent vs. Codelink vs. Applied?

[Ramon Diaz-Uriarte]

Dear Adai,

Thanks a lot for your answer. You actually provide a lot of interesting 
suggestions, and I'll ask about some of these possible options. Yes, I looked 
at the nature Methods and the PNAS paper, but some of the platforms I was 
interested in were not included. The people I've talked to, they all seemed 
happy with the platform they were using, and that is why I was looking for 
possible comparisons.

Best,

R.

On Tuesday 17 May 2005 21:02, Adaikalavan Ramasamy wrote:
> Sorry, I have no experience with any of these arrays.
>
> If you can spend a bit of money, then it might be worth investigating
> their reproducibility (and perhaps the investigation might end up as an
> article too).
>
> I think you might be able to send your samples to these different
> companies and ask them to do the hybridisation for you explaining that
> you are interested in long term commitment if the hybridisation works
> out. They may offer to do so at a special price.
>
> Then unknown to them send some sample along with some repeat aliquots
> (e.g. 5 biological samples x 3 aliquots = 15 "samples"). This way you
> can assess the biological and technical variability when it is done
> under the best procedures.
>
> If you have more money, then give the same samples to someone who is
> relatively new with microarray (e.g. PhD student?). Then calculate the
> variability and compare with above. This would tell you how sensitive
> each platform is to bad handling.
>
> A modification of this is to spike in some genes of known concentration
> or supplying the same sample to many different labs.
>
> The following news articles covers 3 recent studies that compared the
> effect of different platforms and labs. Try scanning them to see if the
> platforms you mentioned are covered by these studies
> http://focus.hms.harvard.edu/2005/May6_2005/comp_bio.shtml
>
> If you do not have the money, then do a literature search and talk to
> many people who have done the array.
>
> Regards, Adai
>
> On Tue, 2005-05-17 at 18:54 +0200, Ramon Diaz-Uriarte wrote:
> > Dear All,
> >
> > We are trying to decide on whether to use Agilent two-color arrays,
> > Codelink arrays or Applied Biosystems arrays (the last two are one-color)
> > for a new study. An advantage of the one-color platforms is that
> > design-related issues (loop, reference, all pairwise, etc) are no longer
> > an issue. This is very relevant in our case because we have 5 groups of
> > very unequal sample sizes and we´ll need to correct for the effect of
> > several covariates, so finding an optimal design seems difficult.
> >
> > I've seen several recent posts in the lists concerning Codelink arrays. I
> > wonder if anybody has any comparison among these platforms (specially if
> > forced to use a common reference design for the two-color arrays), or any
> > experience with the Applied Biosystems arrays.
> >
> > Best,
> >
> > R.

-- 
Ramón Díaz-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
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