[BioC] analysis of HG_U95A vs. HG_U95Av2

[Marc Carlson]

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
>
>   
This is a difficult problem since there are platform specific effects. 
For example, you might think that a probeset which is shared between the
two platforms would be safe to compare, but unfortunately, it will
behave slightly differently on one platform than on the other.  Even
though in theory this is measuring the same thing. 

You could start by just normalizing these two array types in separate
pools.  Then you could take probesets that are supposedly shared between
them and look to see how they are behaving in their respective
conditions.  In general, I expect you will find that shared probesets to
move the same direction on each platform under your experimental
conditions, but that you get different absolute results on one platform
than on another for a given condition.  In other words, both the
condition and the platform will contribute to the overall signal.  The
easiest thing is always to look at one platform at a time, but if you
*must* combine them, grab a statistician 1st to try and help you to do
something sensible.

    good luck,

       Marc