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rohan bareja
▴
200
@rohan-bareja-4905
Last seen 7.2 years ago
Hi Sean,
I am trying to get the gene ids for
genes_new<- unlist(sapply(gpllist[1:3], function(a) {Table(a)[,'Gene
ID']}))
On Monday, 25 November 2013 2:33 PM, Sean Davis <sdavis2@mail.nih.gov>
wrote:
On Mon, Nov 25, 2013 at 2:22 PM, rohan bareja <rohan_1925@yahoo.co.in>
wrote:
Hi Sean,
>
>the answer was really helpful.I am using this to get all the
annotations for gpl in this object ,since there are 438 gpl's in
annotgpl object.
>
>gpllist <- sapply(annotgpl[1:438,1],getGEO,AnnotGPL=TRUE)
>
>But this is a list object, and I am unable to access this using a
Table function.
>
>
Hi, Rohan.
Yes, you'll need to apply the Table() method to each member of the
gpllist; another sapply or an lapply would be useful here.
Sean
basically, I would like to have a table with mapping of gpl and all
its gene ids:
>
>GPL 13 geneid1
>GPL13 geneid2
>GPL 13 geneid3
>
>
>GPL 14 geneid1
>GPL14 geneid2
>GPL 14 geneid3
>
>Thanks,
>Rohan
>
>
>
>
>On Friday, 22 November 2013 6:27 PM, Sean Davis
<sdavis2@mail.nih.gov> wrote:
>
>
>
>
>
>
>On Fri, Nov 22, 2013 at 4:53 PM, Rohan [guest]
<guest@bioconductor.org> wrote:
>
>
>>I would like to get the data for all the genes in the form of Gene
Symbols/Gene ids's mapped to GPL/GSE/GSM/GDS metadata.
>>I have used GEOmetadb package to get this metadata,however I am not
able to find a way to extract all this metadata mapped to genes.
>>
>>Is their any way GEOquery bioconductor package be used for this?
>>
>
>Good question. It has a long-winded answer.
>
>The GEO platform (GPL) is the only GEO entity that stores any
information about gene identity. Other entities (GSM, GSE, GDS) are
linked to GPL rows by an ID column. So, to get information about the
genes represented by an experiment, we need to look at GPL records.
GPL records come in two flavors, the submitter-supplied flavor and the
so-called "Annotation" GPL that has been curated by NCBI GEO. You'll
need to focus on the Annotation GPL since those are the ones with a
standard "Gene ID" column in all of them. The "Annotation" GPLs are
only generated for data sets that have been curated by NCBI GEO,
namely the GDS records. So, we need to get the distinct GPL records
associated with GDS and these will be the entire set of "Annotation"
GPLs. Using GEOmetadb (assuming you have already made a connection,
etc.):
>
>annotgpl = dbGetquery(con,"select distinct GPL from gds")
>
>Now, annotgpl contains the accession numbers (GPL IDs) for all the
Annotation GPLs. You can use these GPL IDs to relate each GPL to GSM,
GDS, and GSE records.
>
>How do you get the information about what genes are on each GPL,
though? You'll need to use GEOquery for that.
>
>gpl = getGEO(annotgpl[1,1],AnnotGPL=TRUE)
>
>gpl is now a GPL object and we can use the Table method to get a data
frame and grab the Gene ID (which is an Entrez Gene ID):
>
>geneids = Table(gpl)[,'Gene ID']
>
>Now, you have the Entrez Gene IDs for all features on the platform
and you can associate those with all the GSM, GDS, and GSE records
attached to the GPL. If you loop over all the GPLs in the annotgpl
data frame, you'll have the information you want, I think.
>
>Unfortunately, this is not a complete answer because it does not
include the submitter-supplied GPLs that do not have any Annotation
GPL available (since NCBI GEO do not curate everything). The
submitter-supplied GPLs do not have a standard vocabulary for what is
include in the columns of the GPL, so there is not an easy way to
automate processing as above.
>
>Hope that helps.
>
>Sean
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>
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