[BioC] analysis of HG_U95A vs. HG_U95Av2

[Ben Bolstad]

My take on the matter (from the very distant past, mind you, so none of
the packaged material there will work now or with any recent version of
the software) is here:

http://bmbolstad.com/misc/mixtureCDF/MixtureCDF.html

The key point there being that the differences between U95A and U95Av2
are fairly small (there is only a relative handful of probesets which
differ between the two, I think something like 25 out of ~12600).

Best,

Ben


On Wed, 2007-07-18 at 18:27 -0400, Alex Tsoi wrote:
> Dear all,
> 
> I have a cancer dataset from GEO that labeled as having the platform GPL 91
> (HG-U95A), and when I use justRMA() to read the data, I realize that the
> GSMs are from HG_U95A and HG_U95Av2, and that gives me the error. I could
> separately analyze the data but I just want to ask if anyone has experience
> or comments about the difference between the two platforms AND could I seem
> the data coming from one platform, and analyze them (eg. by using RMA); of
> course if that's the case I have to "make" R believe that they are coming
> from only one platform. Or what's the most proper way to analyze these kinds
> of data ?
> 
> Greatly appreciate for the help and the comments
> 
> P.S.: this is a cancer dataset, with two types of disease state, and each
> type could be either come from the HG-U95A or HG_U95Av2
>