[BioC] Variable probe binding and its impact on analysis

[Sean Davis]

On Nov 20, 2007 4:00 PM, Srinivas Iyyer <srini_iyyer_bio at yahoo.com> wrote:
> Dear group,
> apologies for asking a general question here. Since
> many microarray specialists are here, I dared to ask.
>
> What is the logic and impact of cross hybridizing
> probes on data analysis in an agilent platform.  There
> are some probes that hybridize to other non-homologous
> genes.  If a probe shows with 100% identity to Gene1
> (G1) from 1-60 bp length, and it shows good identity
> from 4-60 with Gene2.
>
> will these two genes compete to bind to this probe and
> if so will that binding signal be misleading?

Hi, Srini.  I do not think the binding is competitive, but both
targets will potentially contribute to signal.  That said, with oligo
probes, I think this is less of an issue than with cDNA probes.  There
are not, to my knowledge, well-defined protocols for dealing with
oligo arrays in terms of cross-hybridization potential and usability
(i.e., how much is too much).  I suppose it depends some on the
experiment and the hypotheses being tested.  In the end, though, if
there are strong conclusions being drawn from individual probes, it is
probably necessary to validate the findings using another technology.

Sean