[BioC] MGU74A and MGU74Av2

[Ben Bolstad]

You have several options.

1. treat the MGU74a  and MGU74av2 seperately, then try to figure out a
way to combine them.
2. Look at only the common probesets but in this case you will be
thowing away about 2500-3000 probesets (out of about 12600 total
probesets)

Option 1 is doable right now. 

I will have an approach for option 2 in a couple of hours (a local
colleague has been bothering me about this for awhile).

thanks,

Ben


On Fri, 2003-06-20 at 12:47, David O. Nelson wrote:
> On Fri, 2003-06-20 at 11:24, Yongde Bao wrote:
> > David:
> > 
> > Can you tell us how you dealt with the masked genes in MG 74A with rma?
> > 
> 
> I didn't. As I understand RMA (please correct me if I'm wrong here), the
> default approach is to use Ben Bolstad's quantile normalization followed
> by a robust fit of an additive model (y ~ array + probe) to each probe
> set separately.
> 
> So, if you confine your attention to one chip type for your arrays, the
> normalization should go thru OK, and the fact that a particular probe
> set is spectacularly bad in predicting expression levels doesn't affect
> the expression estimates for other probe sets.
>  
> Is that line of reasoning bogus?
> 
> dave
> 
> 
> > Thanks, Yongde Bao
-- 
Ben Bolstad <bolstad at stat.berkeley.edu>