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

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