On Fri, May 28, 2010 at 4:56 AM, Timothy Wu <2huggie@gmail.com> wrote:

> Hi,
>
> I'm using getGEO to obtain the serie GSE18154 and I encounter the following
> error:
>
> > gse18154 <- getGEO("GSE18154")
> Found 1 file(s)
> GSE18154_series_matrix.txt.gz
> trying URL '
>
> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE18154/GSE18154_series_matrix.txt.gz
> '
> ftp data connection made, file length 1891349 bytes
> opened URL
> downloaded 1.8 Mb
>
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
> :
>  scan() expected 'a real', got '"GSM453789"'
> In addition: Warning messages:
> 1: In grepl("^!Series_", dat) : input string 38 is invalid in this locale
> 2: In grepl("^!Series_", dat) : input string 46 is invalid in this locale
> 3: In grepl("^!Sample_", dat) : input string 38 is invalid in this locale
> 4: In grepl("^!Sample_", dat) : input string 46 is invalid in this locale
>
> I think part of the problem may be the extra quotation marks (when
> comparing
> to another matrix file that works), after downloading it and manually
> removing the quotation marks, getGEO load the local file with less
> warnings:
>
> > gse18154 <- getGEO(filename="GSE17308_series_matrix.txt")
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
> :
>  scan() expected 'a real', got 'GSM433039'
>
>
Hi, Timothy.  It is hard to comment without sessionInfo(), but my guess is
that this has to do with the locale you are using.  Your code works fine for
me.  Check the locale and perhaps change it to "C" locale or "en_US" (the
exact terminology depends a bit on OS).  See the help for "locales" for
details.

Sean

> library(GEOquery)
> gse = getGEO("GSE18154")
Found 1 file(s)
GSE18154_series_matrix.txt.gz
trying URL '
ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE18154/GSE18154_series_matrix.txt.gz
'
ftp data connection made, file length 1891349 bytes
opened URL
==================================================
downloaded 1.8 Mb

File stored at:
/var/folders/F+/F+PwkbXqF6WeunvinD8pZk+++TI/-Tmp-//RtmpSCXRVm/GPL9216.soft
>  sessionInfo()
R version 2.12.0 Under development (unstable) (2010-04-30 r51866)
i386-apple-darwin9.8.0

locale:
[1] en_US/en_US/C/C/en_US/en_US

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] GEOquery_2.13.0 RCurl_1.4-1     bitops_1.0-4.1  Biobase_2.9.0

loaded via a namespace (and not attached):
[1] tools_2.12.0

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