Hi all,
I am currently analyzing some arabidopsis thaliana experiments
(ath1121501
GeneChip)
The corresponding annotation package, ath1121501.db, is a little bit
'special' as
there is no ENTREZID map for the chip.
I would like to cheat and create a fake ath1121501ENTREZID for the
environment as a copied instance of ath1121501ACCNUM (in order to use,
for
instance, the genefilter package's function "nsFilter" to deal with
non
annotated, or duplicated probesets)
The problem is that I am not able to create a new entry in the
package:ath112150.db as it is a locked environment. Is there any way
to
temporarily unlock it, do some stuff and lock it again?
(It seems easy to lock environments, using the lockEnvironment
function, but
I did not find an easy way to unlock them)
Thanks in advance
Ariel./
--
Dr. Ariel Chernomoretz
Departamento de Fisica, FCEyN, Universidad de Buenos
Aires,
(1428) Ciudad Universitaria, Ciudad de Buenos Aires,
Argentina.
TE +54 11 4576 3390 ext 817
Fax +54 11 4576 3357
email: ariel@df.uba.ar Webpage:
http://www.df.uba.ar/users/ariel
[[alternative HTML version deleted]]
Hi Ariel,
One solution is that you use the development version of Bioconductor
(BioC 2.5, to be released soon, based on the R-2.10 series).
In the development version of genefilter it looks like the nsFilter()
function has been improved in order to deal properly with the
peculiarity of the ath1121501.db package. Internally it's now
calling a little helper function .findCentralID() (not exported)
in order to determine what's the central ID in the annotation
package:
library(genefilter)
library(hgu95av2.db)
library(ath1121501.db)
> genefilter:::.findCentralID("hgu95av2")
[1] "ENTREZID"
> genefilter:::.findCentralID("ath1121501")
[1] "ACCNUM"
Cheers,
H.
Ariel Chernomoretz wrote:
> Hi all,
> I am currently analyzing some arabidopsis thaliana experiments
(ath1121501
> GeneChip)
> The corresponding annotation package, ath1121501.db, is a little bit
> 'special' as
> there is no ENTREZID map for the chip.
> I would like to cheat and create a fake ath1121501ENTREZID for the
> environment as a copied instance of ath1121501ACCNUM (in order to
use, for
> instance, the genefilter package's function "nsFilter" to deal with
non
> annotated, or duplicated probesets)
>
> The problem is that I am not able to create a new entry in the
> package:ath112150.db as it is a locked environment. Is there any way
to
> temporarily unlock it, do some stuff and lock it again?
> (It seems easy to lock environments, using the lockEnvironment
function, but
> I did not find an easy way to unlock them)
>
> Thanks in advance
> Ariel./
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
Forgot to send my sessionInfo(), sorry:
> sessionInfo()
R version 2.10.0 Under development (unstable) (2009-09-24 r49817)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8
[7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] hgu95av2.db_2.3.5 org.Hs.eg.db_2.3.5 genefilter_1.25.9
[4] ath1121501.db_2.3.5 org.At.tair.db_2.3.5 RSQLite_0.7-2
[7] DBI_0.2-4 AnnotationDbi_1.7.17 Biobase_2.5.8
loaded via a namespace (and not attached):
[1] annotate_1.23.4 splines_2.10.0 survival_2.35-7 tools_2.10.0
[5] xtable_1.5-5
H.
Hervé Pagès wrote:
> Hi Ariel,
>
> One solution is that you use the development version of Bioconductor
> (BioC 2.5, to be released soon, based on the R-2.10 series).
>
> In the development version of genefilter it looks like the
nsFilter()
> function has been improved in order to deal properly with the
> peculiarity of the ath1121501.db package. Internally it's now
> calling a little helper function .findCentralID() (not exported)
> in order to determine what's the central ID in the annotation
> package:
>
> library(genefilter)
> library(hgu95av2.db)
> library(ath1121501.db)
> > genefilter:::.findCentralID("hgu95av2")
> [1] "ENTREZID"
> > genefilter:::.findCentralID("ath1121501")
> [1] "ACCNUM"
>
> Cheers,
> H.
>
>
> Ariel Chernomoretz wrote:
>> Hi all,
>> I am currently analyzing some arabidopsis thaliana experiments
>> (ath1121501
>> GeneChip)
>> The corresponding annotation package, ath1121501.db, is a little
bit
>> 'special' as
>> there is no ENTREZID map for the chip.
>> I would like to cheat and create a fake ath1121501ENTREZID for the
>> environment as a copied instance of ath1121501ACCNUM (in order to
use,
>> for
>> instance, the genefilter package's function "nsFilter" to deal
with non
>> annotated, or duplicated probesets)
>>
>> The problem is that I am not able to create a new entry in the
>> package:ath112150.db as it is a locked environment. Is there any
way to
>> temporarily unlock it, do some stuff and lock it again?
>> (It seems easy to lock environments, using the lockEnvironment
>> function, but
>> I did not find an easy way to unlock them)
>>
>> Thanks in advance
>> Ariel./
>>
>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
Excelent news... (I noticed that there is an 'org.At.tair.db' also
available in the devel version!)
Thanks Herve for the info
A./
PS: I am still curious about the locking/unlocking issue...
2009/10/1 Hervé Pagès <hpages@fhcrc.org>
> Forgot to send my sessionInfo(), sorry:
>
> > sessionInfo()
> R version 2.10.0 Under development (unstable) (2009-09-24 r49817)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] LC_CTYPE=en_CA.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_CA.UTF-8 LC_COLLATE=en_CA.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_CA.UTF-8
> [7] LC_PAPER=en_CA.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] hgu95av2.db_2.3.5 org.Hs.eg.db_2.3.5 genefilter_1.25.9
> [4] ath1121501.db_2.3.5 org.At.tair.db_2.3.5 RSQLite_0.7-2
> [7] DBI_0.2-4 AnnotationDbi_1.7.17 Biobase_2.5.8
>
> loaded via a namespace (and not attached):
> [1] annotate_1.23.4 splines_2.10.0 survival_2.35-7 tools_2.10.0
> [5] xtable_1.5-5
>
>
> H.
>
>
>
> Hervé Pagès wrote:
>
>> Hi Ariel,
>>
>> One solution is that you use the development version of
Bioconductor
>> (BioC 2.5, to be released soon, based on the R-2.10 series).
>>
>> In the development version of genefilter it looks like the
nsFilter()
>> function has been improved in order to deal properly with the
>> peculiarity of the ath1121501.db package. Internally it's now
>> calling a little helper function .findCentralID() (not exported)
>> in order to determine what's the central ID in the annotation
>> package:
>>
>> library(genefilter)
>> library(hgu95av2.db)
>> library(ath1121501.db)
>> > genefilter:::.findCentralID("hgu95av2")
>> [1] "ENTREZID"
>> > genefilter:::.findCentralID("ath1121501")
>> [1] "ACCNUM"
>>
>> Cheers,
>> H.
>>
>>
>> Ariel Chernomoretz wrote:
>>
>>> Hi all,
>>> I am currently analyzing some arabidopsis thaliana experiments
>>> (ath1121501
>>> GeneChip)
>>> The corresponding annotation package, ath1121501.db, is a little
bit
>>> 'special' as
>>> there is no ENTREZID map for the chip.
>>> I would like to cheat and create a fake ath1121501ENTREZID for
the
>>> environment as a copied instance of ath1121501ACCNUM (in order to
use,
>>> for
>>> instance, the genefilter package's function "nsFilter" to deal
with non
>>> annotated, or duplicated probesets)
>>>
>>> The problem is that I am not able to create a new entry in the
>>> package:ath112150.db as it is a locked environment. Is there any
way to
>>> temporarily unlock it, do some stuff and lock it again?
>>> (It seems easy to lock environments, using the lockEnvironment
function,
>>> but
>>> I did not find an easy way to unlock them)
>>>
>>> Thanks in advance
>>> Ariel./
>>>
>>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
--
Dr. Ariel Chernomoretz
Departamento de Fisica, FCEyN, Universidad de Buenos
Aires,
(1428) Ciudad Universitaria, Ciudad de Buenos Aires,
Argentina.
TE +54 11 4576 3390 ext 817
Fax +54 11 4576 3357
email: ariel@df.uba.ar Webpage:
http://www.df.uba.ar/users/ariel
[[alternative HTML version deleted]]
Hi Ariel,
The reason why the arabidopsis chip packages do not have an ENTREZID
mapping is because this is not what these packages are primarily based
upon and we didn't want people to grab those IDs out of habit from
using
the other chip packages. Instead, these packages are based on the
"TAIR" sources which are popular with the community that likes to
study
Arabidopsis. As a result of this, the mapping that you want to use to
filter the results should be the TAIR IDs which for historical reasons
live in the ACCNUM mapping for the arabidopsis packages. Herve beat
me
to the punch, but the nsFilter method in the latest version of the
devel
branch has already been modified to determine what kind of annotation
package you are using and then make the correct decision about what
kind
of mapping it should be using to filter.
If you really want entrez gene IDs for something else, you can get
them
by using the ENTREZID mapping found in the org.At.tair.db package.
All
of the TAIR IDs from your chip package should have a match in that
package which is also primarily based on the TAIR data sources.
I have made a change to the release version of this package to correct
this bug, it should show up online within about a day.
As for unlocking the packages, we strongly discourage that as it can
cause all manner of odd behavior with other packages that depend on
these annotations to produce standard annotations... But if you
really
want to play with "bombs and guns", you should be able to set the
database file to be write-able.
Marc
Ariel Chernomoretz wrote:
> Hi all,
> I am currently analyzing some arabidopsis thaliana experiments
(ath1121501
> GeneChip)
> The corresponding annotation package, ath1121501.db, is a little bit
> 'special' as
> there is no ENTREZID map for the chip.
> I would like to cheat and create a fake ath1121501ENTREZID for the
> environment as a copied instance of ath1121501ACCNUM (in order to
use, for
> instance, the genefilter package's function "nsFilter" to deal with
non
> annotated, or duplicated probesets)
>
> The problem is that I am not able to create a new entry in the
> package:ath112150.db as it is a locked environment. Is there any way
to
> temporarily unlock it, do some stuff and lock it again?
> (It seems easy to lock environments, using the lockEnvironment
function, but
> I did not find an easy way to unlock them)
>
> Thanks in advance
> Ariel./
>
>
