[BioC] MGU74A and MGU74Av2

[Susan G. Hilsenbeck]

A fairly large number of sequences targetted on the MGU74A chip were actually 
the antisense rather than the sense, and therefore the probes were sense 
rather than antisense. When the new version was designed the features (spots) 
used by each of the bad probesets were reshuffled, so that the locations of 
the probe pairs changed completely. In any case, the affected probesets on 
version 1 cannot be used.

A strategy that was used several years ago, when this was initially discovered 
and many people had mixed datasets with both genechips, was to use the 
MGU74Av2 *.cdf but to mask out the affected genes for analyses involving both 
chips types. A file showing the original and replacement probeset ids is 
available from the NetAFFX website.

>===== Original Message From Laurent Gautier <laurent at cbs.dtu.dk> =====
>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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