[BioC] Analyzing expression Affymetrix Hugene1.0.st array

[Steve Lianoglou]

Hi,

Totally agree w/ everything Jim has said (this is usually a smart
thing to do), but just wanted to comment on:
On Fri, Sep 28, 2012 at 11:21 AM, James W. MacDonald <jmacdon at uw.edu> wrote:
[snip]

> I think this becomes a bit more difficult with the Gene ST arrays, as the
> negative controls have a nasty habit of looking not only expressed, but
> differentially expressed. A lot of these controls are supposed to target
> introns, which makes me wonder how much of the total RNA extracted from a
> cell is mRNA for which the introns have yet to be excised.

Instead of such negative control probes, perhaps you (Juan) might know
something about the types of cells you have data from. In particular,
perhaps you can justify identifying a multitude of genes that you know
not to be expressed in these cell types and use some statistics over
their probe expression to rig up a lower bound of your detection
limit.

If you don't know this info, and have no expert to ask, maybe you can
find rna-seq data in cells "close" (using some definition of "close"
that makes you comfortable) and use that to find such non-transcribed
genes.

I guess there's also going to probe (sequence content) effects that
affect the expression readout of these "silent" probes and what not,
but ... if you're going for some heuristic thing that you're not using
as the lynchpin of your study, then perhaps this is passable.

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact