Hi Lavinia.
I'm hoping that most of this is explained in the MAT Smoothing
section at:
http://groups.google.com/group/aroma-affymetrix/web/promoter-tiling-array
In your case, the IPs would be Treatment (you would make + numbers in
the design matrix) and Inputs would be Control (- numbers in
Hi Lavinia.
Yes.
Bandwidth(MAT)=probeWindow(aroma.affymetrix MAT)
Also,
MinProbe(MAT)=nProbes(aroma.affymetrix MAT)
Cheers,
Mark
On 1-Sep-09, at 11:31 AM, Lavinia Gordon wrote:
Hi,
I have some older MAT pure results that I'd like to compare to newer
MAT aroma.affymetrix results.
Thanks Mark, very helpful.
Sorry, one other question.
With MAT (pure), you group your controls + inputs, e.g.
Treatment (1) or Control (0) groups = 111000 for 3ChIP and 3Input
How is this best done with MAT aroma.affymetrix (in the contrast
matrix)?, it isn't immediately clear to me from the
