if(!require('GEOquery')) biocLite('GEOquery')

library(GEOquery)
foo <- getGEO('GSE20986')[[1]] ## since there's only one dataset
show(foo)
## ExpressionSet (storageMode: lockedEnvironment)
## assayData: 54675 features, 12 samples
## ...

Statistics is the grammar of science.
Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science>


On Thu, Feb 13, 2014 at 10:50 AM, Jerry Cholo <jerrycholo@gmail.com> wrote:

> Hi everyone,
>
> I would like to get a data (e.g. "GSE20986") from GEO using getGEO.  And
> then start analyzing the the data by different packages/functions in the
> "biocuonductor" to get the differentially expressed genes.  For the first
> step, I used this
> (
> http://www.bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.R
> )<
> http://www.bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.R
> >
> .
>
> When I ran following line:
>
> gse <-
>
> getGEO(filename=system.file("extdata/GSE8500_family.soft.gz",package="GEOquery"))
>
> I got this error:
>
>
> -----------------------------------------------------------------------------------------------------------------------------------
>
> Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
> invalid 'nlines' argument
>
> In addition: Warning messages:
>
> 1: In file(fname, "r") : file("") only supports open = "w+" and open =
> "w+b": using the former
>
> 2: In file(con, "r") : file("") only supports open = "w+" and open = "w+b":
> using the former
>
> 3: In file(fname, "r") : file("") only supports open = "w+" and open =
> "w+b": using the former
>
>
> -----------------------------------------------------------------------------------------------------------------------------------
>
> May someone send me a script that I could do all these steps to get the
> differentially expressed genes?
>
> Thanks,
>
> Jerry
>
>         [[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]]

