[BioC] Importing data from GEOquery

[Vincent Carey 525-2265]

please read the posting guide before posting.  you should
identify your system and version of R.

i can verify that this problem occurs on windows R 2.7.0
and on mac osx R 2.8.0 r45836 with RCurl 0.8-3 and GEOquery 2.5.0

however example(getGEO) works on those systems, so i wonder
if the problem is with the GSM3612 files rather than GEOquery.
we have no way of verifying that the files on GEO are parseable
short of trying to read them.

---
Vince Carey, PhD
Assoc. Prof Med (Biostatistics)
Harvard Medical School
Channing Laboratory - ph 6175252265 fa 6177311541
181 Longwood Ave Boston MA 02115 USA
stvjc at channing.harvard.edu

On Wed, 25 Jun 2008, Kini, Aditya M wrote:

> Hi,
>
> I am repeatedly getting this error message when I try to import a file from GEO. Here is the code:
>
> > gsm.1 <- getGEO("GSM3612")
> trying URL 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GSM3612&form=text&view=full'
> Content type 'geo/text' length unknown
> opened URL
> downloaded 1.5 Mb
>
> File stored at:
> C:\Users\Aditya\AppData\Local\Temp\Rtmp5ZePB5/GSM3612.soft
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,  :
>   scan() expected 'a real', got '!sample_table_end'
> > gsm.1
> Error: object "gsm.1" not found
>
> Please let me know what the problem is.
>
> Thanks,
> Adi
>
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