Thanks Sean,

That is exactly what I was looking for!

Cheers,
Marcelo


On Thu, May 8, 2014 at 10:15 AM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> On Thu, May 8, 2014 at 8:21 AM, Marcelo Pereira <marcelops@gmail.com>
> wrote:
> > That is all because I am interested in the expression values for some
> pairs
> > of genes.
> >
> > If I had something like this:
> >
> >       GSM278765 GSM278766 GSM278767 ...
> > A1BG   5.459950  5.548725  5.477436 ...
> > NAT2   6.728919  6.329578  6.570104 ...
> > ADA    6.861095  7.005730  7.235361 ...
> > CDH2   9.660035  9.189507  9.740223 ...
> > ...    5.644313  5.898675  5.475838 ...
> > ...    7.838040  7.564335  8.397569 ...
> >
> > Then I could extract lines for the genes of interest (for example, 'A1BG'
> > and 'ADA'), and then plot scatterplots, compute correlation coefficients,
> > etc...
>
> Something like this might work:
>
> plot(exprs(gset[[1]])[fData(gset[[1]])$Gene=='A1BG',])
>
> Sean
>
>
> > The name of the genes for each line is the only detail that is not
> present
> > in my dataset.
> >
> > What am I missing here?
> >
> > Thanks,
> > Marcelo
> >
> >
> >
> > On Thu, May 8, 2014 at 7:42 AM, Marcelo Pereira <marcelops@gmail.com>
> wrote:
> >>
> >> Hello Sean,
> >>
> >> Thanks for your replies.
> >>
> >> I used to download all the CEL files, and then load, normalize and
> >> generate the ExpressionSet output.  All manually, and it was working
> fine!
> >>
> >> Then I found out about doing it automatically using the GEOquery
> library.
> >> And this is what have been taking my hours lately.
> >>
> >> The output of exprs(gset[[1]]) is the initial point where I got stuck
> >> after a few minutes using the GEOquery library, because I have the
> >> expression, but not the gene's names.
> >>
> >>       GSM278765 GSM278766 GSM278767 ...
> >> 1      5.459950  5.548725  5.477436 ...
> >> 10     6.728919  6.329578  6.570104 ...
> >> 100    6.861095  7.005730  7.235361 ...
> >> 1000   9.660035  9.189507  9.740223 ...
> >> 10000  5.644313  5.898675  5.475838 ...
> >> 10001  7.838040  7.564335  8.397569 ...
> >>
> >> After that, I tried to manipulate the output in order to translate 1,
> 10,
> >> 100, 1000, to the actual names of the genes.  And my last resource was
> to
> >> ask here at the forum.
> >>
> >> It is looking good already.  I only need to have an extra column, with
> the
> >> names of the genes.
> >>
> >> Thanks,
> >> Marcelo
> >>
> >>
> >> On Thu, May 8, 2014 at 7:14 AM, Sean Davis <sdavis2@mail.nih.gov>
> wrote:
> >>>
> >>> On Thu, May 8, 2014 at 6:58 AM, Marcelo Pereira <marcelops@gmail.com>
> >>> wrote:
> >>> > Hi Sean,
> >>> >
> >>> > Thanks for your answer!
> >>> >
> >>> > That is great already.
> >>> >
> >>> > I can see the gene's names now:
> >>> >
> >>> >> library(GEOquery)
> >>> >> gset <- getGEO("GSE11024", GSEMatrix=TRUE, AnnotGPL=TRUE)
> >>> >> head(fData(gset[[1]]))$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@mail.nih.gov>
> >>> > wrote:
> >>> >
> >>> >> Hi, Marcelo.
> >>> >>
> >>> >>
> >>> >> On Wed, May 7, 2014 at 8:01 PM, Marcelo Pereira <
> marcelops@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]]
> >>> >> >
> >>> >> > _______________________________________________
> >>> >> > Bioconductor mailing list
> >>> >> > Bioconductor@r-project.org
> >>> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>> >> > Search the archives:
> >>> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>> >>
> >>> >
> >>> >         [[alternative HTML version deleted]]
> >>> >
> >>> > _______________________________________________
> >>> > Bioconductor mailing list
> >>> > Bioconductor@r-project.org
> >>> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>> > Search the archives:
> >>> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >>
> >
>

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