[BioC] Bizarre artifacts in MA plots for ChIP-chip data
Steve Lianoglou
mailinglist.honeypot at gmail.com
Wed Sep 24 20:37:18 CEST 2008
Hi Henrik,
On Sep 24, 2008, at 2:14 PM, Henrik Bengtsson wrote:
> Hi,
>
> should I say welcome to the "microarray" world, or have you this far
> been so fortunate not seeing these "artifacts" before? [no sarcasm].
I guess a "welcome" would be appropriate, more or less :-)
I haven't had to personally deal with the raw expression files up
until very recently.
> The MA artifacts you illustrate are probably one of the most
> frequently observed systematic effects when comparing two
> channels/arrays as you do.
>
> I'm going to keep my answer short and precise:
>
> It *is* because your (non-logged) signals have *offset* that you
> observe these artifact.
I like these types of answers. I'll keep that in mind as I weed
through your refs and other literature.
<snip>
> It was our hope when we wrote those that if read carefully they would
> bring better understanding of the problem.
>
> In the end of the day (or week) you will see that what happens is very
> simple and intuitive.
</snip>
Thanks for the detailed response. I'll put your papers at the top of
my pile to read and come back w/ any Qs (probably sometime next
week ;-).
-steve
--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Cornell Medical College of Cornell University
http://cbio.mskcc.org/~lianos
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