[BioC] Mapping Affymetrix annotations with Bioconductor annotations

[James W. MacDonald]

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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Seattle WA 98105-6099