[BioC] Adding annotations to GSE datasets

[Sean Davis]

On Thu, May 8, 2014 at 6:58 AM, Marcelo Pereira <marcelops at gmail.com> wrote:
> Hi Sean,
>
> Thanks for your answer!
>
> That is great already.
>
> I can see the gene's names now:
>
>> library(GEOquery)
>> gset <- getGEO("GSE11024", GSEMatrix=TRUE, AnnotGPL=TRUE)
>> head(fData(gset[[1]]))$Gene
> [1] A1BG NAT2 ADA  CDH2 AKT3 MED6
> 17098 Levels:  A1BG ABCB6 ABCC5 ABCC9 ABCF2 ABI1 ACOT8 ACTR2 ACTR3 ADA
> ADAM8 AKT3 ... ZNF254
>
> But the data frame only contains these columns.
>
>> names(fData(gset[[1]]))
>  [1] "ID"           "Gene"         "UniGene"      "Description"  "Ensembl*
> Chr" "Start (bp)"
>  [7] "End (bp)"     "Strand"       "ORF"          "SPOT_ID"
>
> Where is the expression information for each gene?

exprs(gset[[1]])

gset is an ExpressionSet, so you should read a bit about
ExpressionSets in the Biobase vignette as well as the help page.

Sean


>
> Thanks,
> Marcelo
>
>
>
> On Thu, May 8, 2014 at 6:24 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>> Hi, Marcelo.
>>
>>
>> On Wed, May 7, 2014 at 8:01 PM, Marcelo Pereira <marcelops at gmail.com>
>> wrote:
>> > Quick question:
>> >
>> > I am trying to import some GEO datasets, and having some issues with the
>> > annotations:
>> >
>> > I can download the GSE dataset using:
>> >
>> > gset <- getGEO("GSE11024", GSEMatrix=TRUE, AnnotGPL=TRUE)
>> >
>> >
>> > However, it will return me a ExpressionSet with the following format:
>> >
>> >               X1    X10    X100   X1000 ...
>> > GSM278765
>> > GSM278766
>> > GSM278767
>> > GSM278768
>> > GSM278769
>> > ...
>>
>> This is not what is returned by GEOquery, so you have done some
>> manipulation (looks like you did a transpose on the expression
>> matrix), it seems.
>>
>> > This is pretty much what I need, but I still need to translate (X1, X10,
>> > X100, X1000, etc...) to the actual names of the genes.
>>
>> library(GEOquery)
>> gset <- getGEO("GSE11024", GSEMatrix=TRUE, AnnotGPL=TRUE)[[1]]
>> head(fData(gset))
>>
>> The gene symbols are in the "Gene" column:
>>
>> genesymbols = fData(gset)$Gene
>>
>> Sean
>>
>>
>> >
>> > Any suggestions?
>> >
>> > Thanks,
>> > Marcelo
>> >
>> >         [[alternative HTML version deleted]]
>> >
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>
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>
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