[BioC] Dealing with probes with high fold change but PA call 0

[Gundala Viswanath]

I have an Affymetrix library which I compute the fold change
and PA call for every probe with Bioconductor.

I found cases where probe may have a high fold change (>= 5)
but the Pa call is 0.

My question is, how can we interpret such cases?
Should we assign the probe fold change to be 0 or 1?

We need to assign values because later we will
perform hierarchical clustering with R hclust().
If we assign "NA" we will have problem with clustering later.



G.V.