[BioC] Taqman array analysis

[Bas Jansen]

Hi James:

On Mon, Sep 1, 2008 at 1:25 PM, James Perkins
<jperkins at biochem.ucl.ac.uk> wrote:
> Hi,
>
>
> Apologies for the long list of questions, I have searched the mailing list
> but can't find much info about these arrays.
>
>
> I am looking at low density PCR cards. They measure the expression levels of
> 96 different transcripts from a very small sample of human or animal tissue.
> There are actually 384 reactions going on but in our case each is done in
> quadruplicate (can be through biological or technical repetition).
>
> I wondered if there was a favoured way to normalise this data. The most
> cited paper I have found is the Vandesompele 2002 paper using the geometric
> mean of a number of control genes, implemented in R in the SLqPCR.
>
> Has anything else been developed that could be used with these cards? I
> guess quantile normalisation is out of the question since this makes some
> assumption that the majority of genes don't change in expression.

As far as I know nothing has been developed in Bioconductor for these cards.
When I analyzed them, I first created an ExpressionSet following the
(excellent!) directions given in the the Biobase vignette 'An
introduction to Bioconductor's ExpressionSet class' by Falcon et al.
Then I processed the normalized data (deltaCt) using the LMGene
package in order to perform gene-by-gene ANOVA and to identify
differentially expressed genes. I have repeated the whole procedure
using different control genes (read: different deltaCt values for the
same gene), but in my case I got the same results with the different
controls. Hope this helps.

Kind regards,
Bas