[BioC] Sc03b_MR_v04 CDF package

[Williams, Alan]

Hi Ludo, James, and others,

There are two separate issues. The first issue is that in some of the
older tiling array library files (bpmap files) the mismatch probe was
incorrectly assigned. For example, the same PM probe sequence may be
present in two locations on the array and each PM probe is associated in
the bpmap file with the same MM probe (rather than the physically
adjacent MM probe). This is a bug and is being fixed. Contact
support at affymetrix.com if you encounter such an issue and need new bpmap
files.

The second issue is that the same physical probe (or PM/MM probe pair
for tiling arrays with MM probes) may be present in the bpmap file more
than once with different genome locations. This is expected as these
probes are not unique in the genome. For example in the newer Drosophila
tiling array such entries exist and are valid. 

Best,
Alan
 
On Wed, Aug 27, 2008 at 1:08 PM, James W. MacDonald
<jmacdon at med.umich.edu
<https://stat.ethz.ch/mailman/listinfo/bioconductor> > wrote:
> Hi Ludo,
>
> Ludo Muller wrote:
>>
>> James, you are right about the erroneous bpmap files. I contacted
>> Affymetrix about this problem and after looking into it, they
confirmed
>> that a lot of the mm probes have the same coordinates as the pm
probes in
>> the bpmap files. They are supposedly working to fix the problem, but
>> couldn't give me an estimate of when they would have a corrected
bpmap
>> file.

Thanks for reporting back.

>
> Interesting. I didn't look into the problem any further than to see
that at
> least one MM probe shares the same (x, y) coordinates (in the cdf)
with
> another MM probe. Although by definition the PM probes would also be
> identical, in this case  they have their own coordinates.
>
> So there are two really good (IMO) possibilities here. First, Affy
just
> blundered here, and the bpmap files are wrong. Apparently whomever you
> talked to at Affy thinks this is the case.
>
> Second, since there are supposed to be probes with on average 10 bases
in
> between, I would have to imagine that there are a lot of probes that
would
> be identical. I don't know if they just blithely tile down probes
regardless
> of the fact that there are many replicated probes, or if they just put
one
> down for each replicate and then point to that one probe for the
duplicates
> in the bpmap file, or if they don't use the probes that aren't unique.
It
> has been argued in offline communications that some permutation of the
above
> is the case, and that we just need to change the code in pdInfoBuilder
to
> account for that.
>
> It has also been recommended that we contact a higher-up at Affy to
get
> confirmation which I haven't yet done, but will do now.

I would suggest that you use the 'Affymetrix Scientific Community
Forums':

  https://www.affymetrix.com/community/forums/index.jspa
<https://www.affymetrix.com/community/forums/index.jspa> 

for this. I quite sure that it will then be read by the "right"
persons.   Posting there will also "document" the issue and is much
easier to refer to and follow up on later.  When I've found mistakes
in the NetAffx annotation files, I've been told to report to the
'NetAffx SDK' forum, so I suggest you use that too.

Cheers

Henrik

 
 
Alan Williams | Sr. Director, Informatics | Informatics
alan_williams at affymetrix.com

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