Yes. PA call means present and absent calls.

My main questions is actually
If a probe have a pa call zero.
What is the reasonable expression value we can assign to it?
NA or zero.


> > 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?
>
> Confused -- Are you computing the fold change between between a probe
> (do you mean "probe set") between two arrays, where only one of the
> arrays has an absent call? To both arrays have an "absent" call?


Correct. Two arrays have absent calls. When both PA=0,
I assign PA=0 for that foldchange.





>
> Where is this fold change coming from? This is where better detail on
> how you processed the data (as asked for above) would be helpful.


>From two arrays, control and test sample.

G.V.









>
> > 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.
>
> If you *really* have missing (NA) data, one option you can consider is
> to to impute the missing values so that you can perform such
> downstream analysis that require complete data .
>
> --
> Steve Lianoglou
> Computational Biologist
> Genentech
>

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