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.