[BioC] Mapping Affymetrix annotations with Bioconductor annotations

[Joao Sollari Lopes]

Hi Jim,

Thanks for your quick reply. Actually I was able to do some kind of 
mapping through the position of the probes in the strips using the files:

zebgene11stdrentrezgprobe_17.1.0.tar.gz 
(http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/17.1.0/entrezg.download/zebgene11stdrentrezgprobe_17.1.0.tar.gz)

and

pd.zebgene.1.1.st (provided by Bioconductor)

The annotations compare very well with each other, however the info 
provided by Affymetrix (available in pd.zebgene.1.1.st) are somewhat 
more complete.

The trouble of working with Affymetrix Array Strip is that there seems 
to be little support in bioconductor for it in what concerns annotation. 
Particularly, because packages "annotate" and "annaffy" seem to work 
only with Affymetrix Chips.

I know I have plenty of reading to do, but is there a best-way to work 
with Array Strips and still use packages "annotate" and "annaffy"? At 
the moment I am using package "oligo".

Thanks,
Joao

On 08/29/2013 03:15 PM, James W. MacDonald wrote:
> Hi Joao,
>
> On Thursday, August 29, 2013 7:07:02 AM, Joao Sollari Lopes wrote:
>> Hi,
>>
>> I am trying to compare the annotations provided by Affymetrix with the
>> ones provided by Bioconductor for
>>
>> Zebrafish Gene 1.1 ST Array Strip
>>
>> I have compared the files
>>
>> zebgene11stdrentrezg.db_17.1.0.tar.gz
>> (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/17.1.0/entrezg.download/zebgene11stdrentrezg.db_17.1.0.tar.gz) 
>>
>
> That file isn't supplied by Bioconductor, it is supplied by MBNI at 
> University of Michigan.
>
> In addition, (if you read what they have on their site to know what 
> you are using) the probesets for that CDF no longer correspond in any 
> way to the original probesets that Affy defined. So comparing the two 
> doesn't make any sense.
>
> Best,
>
> Jim
>
>
>>
>>
>> ZebGene-1_1-st-v1.na33.3.zv9.transcript.csv.zip
>> (http://www.affymetrix.com/Auth/analysis/downloads/na33/wtgene-33_3/ZebGene-1_1-st-v1.na33.3.zv9.transcript.csv.zip) 
>>
>>
>>
>> The trouble is that the first identifies the Units as "100000002_at",
>> "100000006_at", ...,  "84703_at" and the second as "12943944",
>> "12943954", ..., "13276104". Is there an easy way to know which
>> correspond to which?
>>
>> Thanks in advance,
>> Joao Lopes
>> Instituto Gulbenkian de Ciencia, Portugal
>>
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>
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
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