[BioC] Agilent 4100a probe annotation information

[Daniel Brewer]

Sean Davis wrote:
> On Monday 08 January 2007 07:24, Daniel Brewer wrote:
>> Hello,
>>
>> Does anyone have either the sequence information or an annotation table
>> for the Agilent Human 1 array (4100a)?  I am trying to find accurate
>> location information for the probes but the internet seems to draw a
>> blank.  I know that there is a 4100a annotation package but the location
>> info from this is via the gene and so may not be accurate
>> (probe->gene->location).
> 
> Sorry, Daniel.  What is the Agilent human 1 array?  Is it the 44k oligo-based 
> CGH array?  I thought you had mentioned in another email that this was a cDNA 
> array.  Could you just specify how many probes are on the array and whether 
> they are oligos or cDNAs?
> 
> Sean

Don't be sorry.  I am getting very confused myself.    I believe it is
not the 44k oligo-based array and the it is a cDNA array.

The description from the paper where the data comes from:
"Commercial cDNA microarrays (Human 1.0;Agilent Technologies, Palo Alto,
CA) with 12,814 unique clones"

>From the data result files and the corresponding probe IDs I managed to
find the corresponding array in GEO (GPL876,
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL876) which
described it as "Agilent Human 1 cDNA Microarray (G4100A) [layout B]".

I have just noticed this in the description which might shead some light:
"Sourced from Incyte's UniGene 1 and Human Drug Target DNA clone sets".
  So maybe the probe ID are Incyte clone IDs. Might be that is a path I
can follow but I've heard that getting Incyte clone information can be
tricky.

Sorry for the confusion.  Hope that clears things up.  Thanks for the help.


-- 
**************************************************************

Daniel Brewer, Ph.D.

Email: daniel.brewer at icr.ac.uk