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

[Steve Lianoglou]

Hi,

On Fri, Dec 6, 2013 at 8:53 PM, Gundala Viswanath <gundalav at gmail.com> wrote:
> I have an Affymetrix library which I compute the fold change
> and PA call for every probe with Bioconductor.

Without you providing any code to show us what you mean, it's hard to
guess what you have done. Bionconductor is a large ecosystem of
packages, and there are many different ones that could have been used
to process an "affymetrix library" and compute fold changes.

So, please provide the code (or more specific detail) to show us how
your data was processed.

Also, by "PA call" I will assume that you mean "present / absent"
call, but for future reference it is very common to first use the
whole word/phrase before you use an acronym for it, even if you think
the acronym is extremely obvious.

> 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?

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.

> 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