[BioC] presence/absence call using oligo array?

[Sean Davis]

On 1/13/06 12:49 PM, "xpeng" <xpeng at utk.edu> wrote:

> Hi Amy,
> 
> Thanks for the reply.
> 
> You are right. The uninfected tissue is a blank, in theory. But the real
> problem is that some probes cross-hybridize with house RNAs. I do not know the
> oligo sequence yet. They know that there are more host RNAs than parasite RNAs
> in the sample from the infected tissue, but not sure the percentage.
> 
> Yes, they are 2-color arrays. The problem here is what to compare. It was
> suggested to find genes with intensities higher than their own backgrounds,
> say 4-fold higer, but I doubt it. I appreciate more inputs on the consequences
> if it is done this way.

Signals above background in the infected sample could be due to at least
three possibilities:

1)  Hybridization by the parasite RNA
2)  Cross-hyb by the host RNA in the uninfected state
3)  Additional cross-hyb by host RNA due to the infection (upregulation of
genes not highly expressed in the uninfected state).

I agree with Amy that the best you can probably do is to look for
differentially-expressed genes between your uninfected host and the infected
sample.  I also agree with Amy that using absolute intensities as a measure
of "expression" is probably not possible with most existing long-oligo
technologies (although some new technologies like illumina seem to be
working somewhat for that).

Sean