On Mon, Jun 28, 2010 at 3:56 PM, Jeremiah H. Savage <
jeremiahsavage@gmail.com> wrote:

> I'm working with some data sets which have several platforms, but would
> like
> to just work with data from one platform at a time.
>
>
Hi, Jeremiah.

library(GEOquery)
gsedat = getGEO("GSE5720")
names(gsedat)
[1] "GSE5720-GPL96_series_matrix.txt.gz"
"GSE5720-GPL97_series_matrix.txt.gz"

gsedat[[1]] is, then, and ExpressionSet and includes only GPL96 platform
data.  gsedat[[2]] is an ExpressionSet and contains only GPL97 data.

Hope that helps.

Sean



> The code below does NOT work, but it is where I'm at. Can somebody give me
> a
> hint on how to modify the lapply() to do what i would like?
>
> Thanks,
> Jeremiah
>
>
> ----------------
> library(GEOquery)
> geodata <- parseGEO("GSE5720.soft")
> gplnames <- names(GPLList(geodata))
> j <- 1
> while(j <= length(gplnames))
>  {
>    gsmdata <- lapply(GSMList(geodata), function(x) {
>      gplnames[j] == Meta(x)$platform_id   # this line does nothing,
>                                        # I would like to alter it so only
>                                        # one platform is applied.
>    })
>
>    # would like 'gsmdata' to now hold half of data
>    # in 'geodata', but it holds all of the data
>    j <- j+1
>  }
>
>        [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

