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

[Steve Lianoglou]

Hi,

On Sat, Dec 7, 2013 at 3:28 PM, Gundala Viswanath <gundalav at gmail.com> wrote:
> 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.

Since you didn't directly answer my question(s), I'll return the favor ;-)

At this stage of the "affy array game," I think you'd need a very good
reason to choose to preprocess your data with something other than
RMA.

So, since RMA doesn't use P/A calls, and pre-processing your data w/
RMA would give you something else besides either NA or 0, I wouldn't
pick either option you propose.

How about simply RMA normalizing your data and use that output for
downstream analysis (clustering, or whatever else you're trying to
do).

If you still *really* want an answer to dealing with the absence
calls, you will find many hits (some publications) if you run a google
search for:

"rma present absent calls"

HTH,
-steve

-- 
Steve Lianoglou
Computational Biologist
Genentech