Hi,
I noticed that when I obtain eset from GEO matrix file via GEOquery,
the
result obtained from limma analysis includes the annotation
information.
However, eset obtained from CEL files via ReadAffy() and GCRMA
threestep()
do not include those annotations. How do I infuse the annotations into
eset
(preferred) before limma analysis? Or maybe during limma result if
that is
more proper. The platform is U133 plus 2.
Any help appreciated, thank in advance.
Timothy
[[alternative HTML version deleted]]
On Thu, Oct 28, 2010 at 5:44 AM, Timothy Wu <2huggie@gmail.com> wrote:
> Hi,
>
> I noticed that when I obtain eset from GEO matrix file via GEOquery,
the
> result obtained from limma analysis includes the annotation
information.
> However, eset obtained from CEL files via ReadAffy() and GCRMA
threestep()
> do not include those annotations. How do I infuse the annotations
into eset
> (preferred) before limma analysis? Or maybe during limma result if
that is
> more proper. The platform is U133 plus 2.
>
> Any help appreciated, thank in advance.
>
>
Hi, Timothy. The easiest way to do this will depend on the details of
the
workflow you are using. If you can provide those details, answering
your
question will be simpler. To answer directly, though, you simply need
to
fill the featureData slot of the eSet with the annotation information.
Sean
[[alternative HTML version deleted]]
On Thu, Oct 28, 2010 at 6:34 PM, Sean Davis <sdavis2@mail.nih.gov>
wrote:
>
>
> On Thu, Oct 28, 2010 at 5:44 AM, Timothy Wu <2huggie@gmail.com>
wrote:
>
>> Hi,
>>
>> I noticed that when I obtain eset from GEO matrix file via
GEOquery, the
>> result obtained from limma analysis includes the annotation
information.
>> However, eset obtained from CEL files via ReadAffy() and GCRMA
threestep()
>> do not include those annotations. How do I infuse the annotations
into
>> eset
>> (preferred) before limma analysis? Or maybe during limma result if
that is
>> more proper. The platform is U133 plus 2.
>>
>> Any help appreciated, thank in advance.
>>
>>
> Hi, Timothy. The easiest way to do this will depend on the details
of the
> workflow you are using. If you can provide those details, answering
your
> question will be simpler. To answer directly, though, you simply
need to
> fill the featureData slot of the eSet with the annotation
information.
>
> Sean
>
Hi Sean,
I am not sure what the workflow you're referring to.
This is how I obtain the eset:
==
library(affy)
library(affyPLM)
affybatch <- ReadAffy()
eset <<- threestep_gcrma(affybatch)
==
Are there package that I can use to fill the featureData? I am not
very
skilled in R and what you says looks intimidating.
Timothy
>
>
[[alternative HTML version deleted]]
On Thu, Oct 28, 2010 at 7:44 AM, Timothy Wu <2huggie@gmail.com> wrote:
> On Thu, Oct 28, 2010 at 6:34 PM, Sean Davis <sdavis2@mail.nih.gov>
wrote:
>
> >
> >
> > On Thu, Oct 28, 2010 at 5:44 AM, Timothy Wu <2huggie@gmail.com>
wrote:
> >
> >> Hi,
> >>
> >> I noticed that when I obtain eset from GEO matrix file via
GEOquery, the
> >> result obtained from limma analysis includes the annotation
information.
> >> However, eset obtained from CEL files via ReadAffy() and GCRMA
> threestep()
> >> do not include those annotations. How do I infuse the annotations
into
> >> eset
> >> (preferred) before limma analysis? Or maybe during limma result
if that
> is
> >> more proper. The platform is U133 plus 2.
> >>
> >> Any help appreciated, thank in advance.
> >>
> >>
> > Hi, Timothy. The easiest way to do this will depend on the
details of
> the
> > workflow you are using. If you can provide those details,
answering your
> > question will be simpler. To answer directly, though, you simply
need to
> > fill the featureData slot of the eSet with the annotation
information.
> >
> > Sean
> >
>
> Hi Sean,
>
> I am not sure what the workflow you're referring to.
>
> This is how I obtain the eset:
>
> ==
> library(affy)
> library(affyPLM)
>
> affybatch <- ReadAffy()
> eset <<- threestep_gcrma(affybatch)
> ==
>
> Are there package that I can use to fill the featureData? I am not
very
> skilled in R and what you says looks intimidating.
>
>
Hi, Timothy. You could look at the the AnnotationDbi package
vignette: AnnotationDbi:
How to use the ".db" annotation packages. Also, you should look at
the
annotate bioconductor package.
Sean
[[alternative HTML version deleted]]
Hi Timothy,
It sounds like you might just be asking how to set the annotation slot
on the ExpressionSet object? You have not given us a lot of
information, so it is hard to know. But if that is the case, then you
might also try:
library(Biobase)
openVignette()
Or just go here:
http://www.bioconductor.org/help/bioc-
views/release/bioc/html/Biobase.html
Or look at the manual page for ExpressionSets:
?ExpressionSet
And learn about the annotation() accessor method that is defined for
these.
Marc
On 10/28/2010 04:48 AM, Sean Davis wrote:
> On Thu, Oct 28, 2010 at 7:44 AM, Timothy Wu <2huggie at gmail.com>
wrote:
>
>
>> On Thu, Oct 28, 2010 at 6:34 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote:
>>
>>
>>>
>>> On Thu, Oct 28, 2010 at 5:44 AM, Timothy Wu <2huggie at gmail.com>
wrote:
>>>
>>>
>>>> Hi,
>>>>
>>>> I noticed that when I obtain eset from GEO matrix file via
GEOquery, the
>>>> result obtained from limma analysis includes the annotation
information.
>>>> However, eset obtained from CEL files via ReadAffy() and GCRMA
>>>>
>> threestep()
>>
>>>> do not include those annotations. How do I infuse the annotations
into
>>>> eset
>>>> (preferred) before limma analysis? Or maybe during limma result
if that
>>>>
>> is
>>
>>>> more proper. The platform is U133 plus 2.
>>>>
>>>> Any help appreciated, thank in advance.
>>>>
>>>>
>>>>
>>> Hi, Timothy. The easiest way to do this will depend on the
details of
>>>
>> the
>>
>>> workflow you are using. If you can provide those details,
answering your
>>> question will be simpler. To answer directly, though, you simply
need to
>>> fill the featureData slot of the eSet with the annotation
information.
>>>
>>> Sean
>>>
>>>
>> Hi Sean,
>>
>> I am not sure what the workflow you're referring to.
>>
>> This is how I obtain the eset:
>>
>> ==
>> library(affy)
>> library(affyPLM)
>>
>> affybatch <- ReadAffy()
>> eset <<- threestep_gcrma(affybatch)
>> ==
>>
>> Are there package that I can use to fill the featureData? I am not
very
>> skilled in R and what you says looks intimidating.
>>
>>
>>
> Hi, Timothy. You could look at the the AnnotationDbi package
> vignette: AnnotationDbi:
> How to use the ".db" annotation packages. Also, you should look at
the
> annotate bioconductor package.
>
> Sean
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
>
Dear BioC users,
I performed different hypergometric tests on my data regarding GO
terms
and KEGG pathways. With GO resukt I can use the probeSetSummary
function to
retrieve the gene list associated to each significant category.
However this function does not work if I apply the HG test using
KEGGHyperGParams because the results are not of GOHyperGResult
class... Is
there any equivalent KEGG function to get those genes list?
WIth advanced thanks for your help.
Cl?mentine
--
Cl?mentine Dressaire
Post-doctoral research fellow
Control of gene expression lab
ITQB - Instituto de Tecnologia Qu?mica e Biol?gica
Apartado 127, Av. da Rep?blica
2780-157 Oeiras
Portugal
+351 214469562
Hi Cl?mentine,
I don't know, if such a function exists. I use two little helper
functions to retrieve probe IDs or gene symbols of genes in a
genelist, that are associated with a KEGG ID:
KEGG2genes = function(KEGGID, genelist, db){
require(paste(db, "db", sep="."), character.only = TRUE)
l = vector("list")
for (i in 1:length(KEGGID)){
kegg = as.matrix(unlist(mget(KEGGID[i], get(paste(db, "PATH2PROBE",
sep="")), ifnotfound=NA)))
l[[i]] = genelist[is.element(genelist,kegg[,1])]
}
names(l)=KEGGID
l
}
KEGG2symbol = function(KEGGID, genelist, db){
l = vector("list")
for (i in 1:length(KEGGID)){
id = unlist(KEGG2genes(KEGGID=KEGGID[i], genelist=genelist, db=db))
l[[i]] = as.matrix(mget(id, get(paste(db, "SYMBOL", sep="")),
ifnotfound=NA))
}
names(l)=KEGGID
l
}
where "KEGGID" is a character vector of your KEGGID(s) you are
interested in, "genelist" is a character vector containing the probe
IDs/probeset IDs of your genelist you used to create the
KEGGHyperGResult and "db" is a character vector with the annotation
database for your array without the .db extension (e.g.
db="hgu133plus" for the affy U133+ 2.0 array). As a result you get a
matrix containing the probeIDs and genesymbols for each KEGGID stored
in a list. It might not be the most elegant way, but it works.
Kind regards,
Mike
-----Urspr?ngliche Nachricht-----
Von: "Cl?mentine Dressaire" <clementinedressaire at="" itqb.unl.pt="">
Gesendet: 29.10.2010 13:27:44
An: bioconductor at stat.math.ethz.ch
Betreff: [BioC] retrieve genes names after KEGG hypergeometric test
>
>Dear BioC users,
>
>
>
>I performed different hypergometric tests on my data regarding GO
terms
>
>and KEGG pathways. With GO resukt I can use the probeSetSummary
function to
>
>retrieve the gene list associated to each significant category.
>
>However this function does not work if I apply the HG test using
>
>KEGGHyperGParams because the results are not of GOHyperGResult
class... Is
>
>there any equivalent KEGG function to get those genes list?
>
>
>
>WIth advanced thanks for your help.
>
>
>
>Cl?mentine
>
>
>
>--
>
>Cl?mentine Dressaire
>
>Post-doctoral research fellow
>
>Control of gene expression lab
>
>ITQB - Instituto de Tecnologia Qu?mica e Biol?gica
>
>Apartado 127, Av. da Rep?blica
>
>2780-157 Oeiras
>
>Portugal
>
>+351 214469562
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
>Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
Hi Mike,
Could ou explain me the difference between the db and "db" you are
using?
If db is the character vector with the annotation database for your
array
without the .db extension, then what does db represent?
Again thanks for your help,
Cl?mentine
On Fri, 29 Oct 2010 14:23:00 +0200 (CEST), "Mike Walter"
<michael_walter at="" email.de=""> wrote:
> Hi Cl?mentine,
>
> I don't know, if such a function exists. I use two little helper
functions
> to retrieve probe IDs or gene symbols of genes in a genelist, that
are
> associated with a KEGG ID:
>
> KEGG2genes = function(KEGGID, genelist, db){
> require(paste(db, "db", sep="."), character.only = TRUE)
> l = vector("list")
> for (i in 1:length(KEGGID)){
> kegg = as.matrix(unlist(mget(KEGGID[i], get(paste(db, "PATH2PROBE",
> sep="")), ifnotfound=NA)))
> l[[i]] = genelist[is.element(genelist,kegg[,1])]
> }
> names(l)=KEGGID
> l
> }
>
> KEGG2symbol = function(KEGGID, genelist, db){
> l = vector("list")
> for (i in 1:length(KEGGID)){
> id = unlist(KEGG2genes(KEGGID=KEGGID[i], genelist=genelist, db=db))
> l[[i]] = as.matrix(mget(id, get(paste(db, "SYMBOL", sep="")),
> ifnotfound=NA))
> }
> names(l)=KEGGID
> l
> }
>
> where "KEGGID" is a character vector of your KEGGID(s) you are
interested
> in, "genelist" is a character vector containing the probe
IDs/probeset
IDs
> of your genelist you used to create the KEGGHyperGResult and "db" is
a
> character vector with the annotation database for your array without
the
> .db extension (e.g. db="hgu133plus" for the affy U133+ 2.0 array).
As a
> result you get a matrix containing the probeIDs and genesymbols for
each
> KEGGID stored in a list. It might not be the most elegant way, but
it
> works.
>
> Kind regards,
>
> Mike
>
> -----Urspr?ngliche Nachricht-----
> Von: "Cl?mentine Dressaire" <clementinedressaire at="" itqb.unl.pt="">
> Gesendet: 29.10.2010 13:27:44
> An: bioconductor at stat.math.ethz.ch
> Betreff: [BioC] retrieve genes names after KEGG hypergeometric test
>
>>
>>Dear BioC users,
>>
>>
>>
>>I performed different hypergometric tests on my data regarding GO
terms
>>
>>and KEGG pathways. With GO resukt I can use the probeSetSummary
function
>>to
>>
>>retrieve the gene list associated to each significant category.
>>
>>However this function does not work if I apply the HG test using
>>
>>KEGGHyperGParams because the results are not of GOHyperGResult
class...
Is
>>
>>there any equivalent KEGG function to get those genes list?
>>
>>
>>
>>WIth advanced thanks for your help.
>>
>>
>>
>>Cl?mentine
>>
>>
>>
>>--
>>
>>Cl?mentine Dressaire
>>
>>Post-doctoral research fellow
>>
>>Control of gene expression lab
>>
>>ITQB - Instituto de Tecnologia Qu?mica e Biol?gica
>>
>>Apartado 127, Av. da Rep?blica
>>
>>2780-157 Oeiras
>>
>>Portugal
>>
>>+351 214469562
>>
>>_______________________________________________
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>>Search the archives:
>>http://news.gmane.org/gmane.science.biology.informatics.conductor
