[BioC] PCR Validation threshold in dChip normalized data

[Sean Davis]

On Thu, Sep 4, 2008 at 8:01 AM, Benjamin Otto <b.otto at uke.uni-hamburg.de> wrote:
> Hi,
>
> Given a dataset for Affymetrix arrays normalized with mas5 or rma we usually
> made the experience that signals below 80 (6,3 in log2 format) are hard to
> validate with PCR.
>
> Can somebody tell me, how I can judge on dChip normalized data in a analog
> way? Where can I draw a threshold to tell, which signal has good chances to
> withstand a verification with with PCR or even on protein level? And which
> signals usually indicate a much to low expression level?

I don't think this is an answerable question, exactly.  See Rafael
Irizarry's work on gene expression barcoding.

http://www.ncbi.nlm.nih.gov/pubmed/17906632

In short, each probeset has a different threshold for expression,
potentially.  Also, keep in mind that PCR, while held out as a "gold
standard" is not without its own biases.  Finally, for proteins, all
bets are off, as there are a number of highly relevant mechanisms for
regulation of protein expression that occur after transcription.

Not really an answer, but it is reality, I think.

Sean