Hello,
I know NCBI provides annotation for the GEO platforms associated with
the
sets they host, but for platforms where bioconductor packages are
available, I would prefer to use those. I am looking for a table
like:
...
GPL96 hgu133a
GPL97 hgu133b
...
Where one column is the NCBI GEO platform identifier and another
column is
the package name (where available) you would use with bioclite to
retrieve annotation information.
Before I set out to create such a table of equivalences for my
project, I
thought I'd ask if anyone else had ever bothered to do so and might be
willing to share.
Regards,
Lynn Miller
miller at accelrys.com
On Sun, Mar 2, 2008 at 11:12 AM, Lynn Miller <miller at="" accelrys.com="">
wrote:
> Hello,
>
> I know NCBI provides annotation for the GEO platforms associated
with the
> sets they host, but for platforms where bioconductor packages are
> available, I would prefer to use those. I am looking for a table
like:
>
> ...
> GPL96 hgu133a
> GPL97 hgu133b
> ...
>
> Where one column is the NCBI GEO platform identifier and another
column is
> the package name (where available) you would use with bioclite to
> retrieve annotation information.
>
> Before I set out to create such a table of equivalences for my
project, I
> thought I'd ask if anyone else had ever bothered to do so and might
be
> willing to share.
We have been working on extending the ability to query GEO for
metadata. Jack Zhu from our group has put together this affy-centric
list which we will be incorporating into the GEO metadata tools, but
those are still not quite ready for prime time. If others have
platform mappings that they are willing to share, that would be great,
as we are trying to compile the same list that Lynn was asking about.
ath1121501 - GPL198
ag - GPL71
celegans - GPL200
drosophila2 - GPL1322
drosgenome1 - GPL72
hu6800 - GPL80
hcg110 - GPL74
hgfocus - GPL201
hu35ksuba - GPL98
hu35ksubb - GPL99
hu35ksubc - GPL100
hu35ksubd - GPL101
hgu133plus2 - GPL570
hgu133a - GPL96
hgu133b - GPL97
hgu133a2 - GPL571
hgu95a - GPL91
hgu95av2 - GPL91
hgu95b - GPL92
hgu95c - GPL93
hgu95d - GPL94
hgu95e - GPL95
u133x3p - GPL1352
moe430a - GPL4032
moe430b - GPL339
mouse4302 - GPL340
mouse430a2 - GPL1261
mu11ksuba - GPL75
mu11ksubb - GPL76
mu19ksuba - GPL77
mu19ksubb - GPL78
mu19ksubc - GPL79
mgu74a - GPL32
mgu74av2 - GPL81
mgu74b - GPL33
mgu74bv2 - GPL82
mgu74c - GPL34
mgu74cv2 - GPL83
rae230a - GPL341
rae230b - GPL342
rat2302 - GPL1355
rgu34a - GPL85
rgu34b - GPL86
rgu34c - GPL87
rnu34 - GPL88
rtu34 - GPL89
xenopuslaevis - GPL1318
yeast2 - GPL2529
ygs98 - GPL90
zebrafish - GPL1319
