[BioC] RNA degradation tends & options for analysis

[Ben Bolstad]

An alternative way to the pairs() method mentioned below is 

MAplot(myAffyBatch,pairs=TRUE)

which will give pairwise MA plots (which tend to be a little more useful
for looking at things in an Y vs X type manner). However, once you get
beyond a relatively small number of arrays this plot becomes unwieldy.
In that case you might consider using it this way:

MAplot(myAffyBatch)

in this case each array will be MA plotted against a "reference" array
created using all the chips in the dataset.

Ben


On Thu, 2006-02-23 at 11:25 -0500, Naomi Altman wrote:
> One thing I find very useful is to look at
> 
> pairs(pm(myAffydata))
> 
> (This takes a while, since you are plotting lots of probes, and I 
> usually put in lower.panel=NULL to get only the upper triangle of plots.)
> 
> If the arrays are comparable, then most of the data should cluster 
> pretty tightly on the diagonal.
> 
> Incidentally, if some ambitious person would write a pairs routine 
> for hexbin, that would be both faster and more informative.
> 
> --Naomi
>