[BioC] missing probe_id in ath1121501.db

[Stefan Bleuler]

Hi Marc

Thank your very much for your research. A fix would be great. In the 
meantime I will just treat this probe_id as having no annotation in any 
category.

Stefan

> Hi Stefan,
>
> I have done some detective work and tracked this down for you.  The
> basic problem here seems to be that for this one probe there is no data
> whatsoever coming from  tair for ANY of the genes that map to it
> (probeset "245651_s_at").  According the sources I have, affy matches
> this probeset matches 5 loci IDs and TAIR does not provide data for any
> of them.  I agree with you though that the probe should still be present
> and will look into a correction for this.
>
>    Marc
>
> On 02/13/2012 12:23 AM, Stefan Bleuler wrote:
>> Hi,
>>
>> I am working with the Bioconductor annotation package for the
>> Arabidopsis thaliana GeneChip ATH1 and have found a strange difference
>> between version 2.7 and versions 2.8 or 2.9.
>>
>> In 2.7:
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("ath1121501.db")
>> library("ath1121501.db")
>> length(as.list(toggleProbes(ath1121501ACCNUM,"all")))
>>
>> produces the following output:
>> [1] 22810
>>
>> In 2.8 or 2.9 the same code produces the following output:
>> [1] 22809
>>
>> Comparing the lists of probe_ids shows that the probe_id 245651_s_at
>> is present in 2.7 and not present in 2.8 or 2.9. I know that the
>> annotations for a given probe_id can change with updates but why would
>> a probe_id be removed? This probe_id is still present in the latest
>> annotation files provided by Affymetrix.
>>
>> Thanks for any idea.
>>
>> Stefan Bleuler
>>
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