[BioC] Bizarre artifacts in MA plots for ChIP-chip data

[Steve Lianoglou]

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