[BioC] presence/absence call using oligo array?

[xpeng]

Thanks a lot.

What are the arrays or other technologies to survey the presence/absence of 
genes in a large scale? I noticed that Winzeler's lab published a paper using 
a Affy-like custom-made, high-density oligo array (Le Roch et al, Science, 
301:1503-1508).

Best,
Xinxia



>===== Original Message From Sean Davis <sdavis2 at mail.nih.gov> =====
>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