[BioC] MGU74A and MGU74Av2

[David O. Nelson]

Our experience with MGU74A and Av2 chips:

As I recall, the MGU74A and Av2 have a different number of probe sets!
Also, while there is substantial overlap in affy IDs:

1. there are probe set names in A that are not in Av2 (expected), and
2. there are probe set names in A2 that are not in A (NOT expected).

We preprocessed the A and Av2 chips separately, because there was some
confusion in RMA about which CDF environment to use for the A and Av2
chips.

(I don't recall the details now, and it was never clear whether some
biologist had edited the CEL file to change the name of the CDF file or
not.)

In any event, BE CAREFUL when combining v1 and v2 chips!

dave

On Thu, 2003-06-19 at 21:46, Laurent Gautier wrote:
> On Fri, Jun 20, 2003 at 02:21:51PM +1000, Matthew Hobbs wrote:
> > Hi,
> > 
> > I have some cel files from experiments using the Affy MGU74A chip and some 
> > from experiments  using the MGU74Av2 chip.  Am I right in thinking that 
> > MGU74A and MGU74Av2  are actually the same chip described differently  
> > (because some probesets were originally designed wrongly)?  
> 
> I believe that v2 stands for "version 2" which means some improvement
> was thrown in.
> 
> > 
> > I wish to treat all this data together.  Can I use theMGU74Av2 CDF to make a 
> > single Affybatch object containing both sorts of data?   If not how should I 
> > proceed?
> 
> If the differences between those two guys and the ones between U95A and U95v2
> are comparable, a simple way should be to have an AffyBatch which is the
> "intersection" between the probe sets in both chips. To achieve this,
> you will need the probes sequences files (should be available at
> www.affymetrix.com) and the .CDF files (or corresponding 'cdfenvs').
> Using these four elements, you will craft a cdfenv that is the intersection
> of the two others (the functions xy2indices and indices2xy should be handy
> to shuttle from the x/y coordinates in the sequence files to the indices
> (NOTE: add 1 to the x/y in the sequence file. The indexing starts at 0
> in Affymetrix files !!!!!)).
> If you are lucky, you won't have to shuffle the values in the 'exprs'
> matrix, but you'd better be prepared to do it...
> 
> 
> Hopin' it helps,
> 
> 
> L.
> 
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-- 
David O. Nelson <daven at llnl.gov>
LLNL