[BioC] Importing data from GEOquery

[Vincent Carey 525-2265]

On Wed, 25 Jun 2008, Sean Davis wrote:

> >
> > 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, Vince, for checking into the problem.  It looks like those
> files have a multibyte character (that was supposed to be a degree
> symbol, from the looks of it) that is problematic in at least some
> locales.  I don't know of an easy way to fix the problem, as the files
> at NCBI are supposed to all be in the same character encoding (UTF-8).
>  If anyone knows of a solution, let me know.
>
>

i just checked it on a more recent version of R and we get more info:

downloaded 1.5 Mb

File stored at:
/tmp/RtmpjQn5oh/GSM3612.soft
Error in make.names(col.names, unique = TRUE) :
  invalid multibyte string 29
In addition: Warning messages:
1: In grep("!\\w+_table_begin", txt[i], perl = TRUE) :
  input string 1 is invalid in this locale
2: In grep("!\\w+_table_begin", txt[i], perl = TRUE) :
  input string 1 is invalid in this locale
3: In grep("^#", txt, perl = TRUE) :
  input string 42 is invalid in this locale
4: In grep("^#", txt, perl = TRUE) :
  input string 67 is invalid in this locale
5: In grep("!\\w*_", txt, perl = TRUE, value = TRUE) :
  input string 42 is invalid in this locale
6: In grep("!\\w*_", txt, perl = TRUE, value = TRUE) :
  input string 67 is invalid in this locale
7: In grep(leader, txt) : input string 42 is invalid in this locale
8: In grep(leader, txt) : input string 67 is invalid in this locale
> sessionInfo()
R version 2.8.0 Under development (unstable) (--)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
[1] GEOquery_2.5.0 RCurl_0.9-3    Biobase_2.1.7

while sean has diagnosed the problem, i report the sessionInfo() because the locale
may also contribute to problems in such endeavors.  people reporting data read problems
should take care to provide all this information in the future.

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