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).
Any help would be gratefully received as I am finding this
frustrating.
Thanks
--
**************************************************************
Daniel Brewer, Ph.D.
Email: daniel.brewer at icr.ac.uk
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
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
On Monday 08 January 2007 08:50, Daniel Brewer wrote:
> 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.
So, from your files, you will need to find some public identifier. Is
there
no Genbank accession number or IMAGE clone identifier in your files?
If not,
then you could contact Agilent directly for assistance.
Sean
Hi Daniel,
The data isn't publicly available that I know of, only the sequence
they
claim are the best matches.
Fortunately, it is available they're making it available to the people
who are buying the chips (minus some of the control sequences):
http://earray.chem.agilent.com. I think you might need to contact your
sales rep to get an account of someone at your university who's a
"site
administrator" could create an account for you. They also have more
up-
to-date gene annotations there, although I tend to prefer the
bioconductor ones.
Worse case, I could try to get those sequences for you.
Francois
On Mon, 2007-01-08 at 12:24 +0000, 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).
>
> Any help would be gratefully received as I am finding this
frustrating.
>
> Thanks
>
