[BioC] getGEO function to load files from other locations than GEO ?

[Wolfgang Raffelsberger]

Dear list,

Sorry to bug you again on the issue of using the "getGEO()" function to 
load files from other locations than GEO...

Sean Davis a écrit :
> See the help for getGEO.  There is a filename argument that does exactly what 
> you are describing.  
>
> Sean
>   

I tried to spicify the file using the filname-argument :

 > in.file <- "GSM180487.txt"             # just picking an example of 
an original GEO downloaded &decompressed file
 > deGEO1 <- getGEO(filename=in.file )      # i.e., from the directory 
with my file...
Error in switch(as.character(first.entity[1]), sample = { :
        argument is missing, with no default

This happens both on Linux & Windows (see sessionInfo at end of message)
.. and the same error occurs when pasting path & file.name :

 > wdir <- getwd()
 > deGEO1 <- getGEO(filename=paste(wdir,in.file,sep="/") )
Error in switch(as.character(first.entity[1]), sample = { :
        argument is missing, with no default
or with :
 > deGEO1 <- getGEO(filename=paste("file:/",wdir,in.file,sep="/") )
Error in switch(as.character(first.entity[1]), sample = { :
        argument is missing, with no default

So, when checking getGEO or taking the code apart I can opne the open 
the connection with :
 > con <- file(paste(wdir,in.file,sep="/"), "r")         # seems to work OK
 > ret <- parseGEO(con, GSElimits=NULL)       # as if getGEO would call 
it ..
Error in switch(as.character(first.entity[1]), sample = { :
        argument is missing, with no default 

Further checking parseGEO that holds the switch(...) experssion cited in 
the error message I got now stuck, when trying to see what  
findFirstEntity() does I get :
 >  findFirstEntity(con)
Error: could not find function "findFirstEntity"


Bottomline, initially I thought the problem is improper syntax of the 
character-string for path & file to be read, so I've tried lots of 
combinations with in-path and '/'s.  But now I'm not sure any more if 
this is really the problem ...
Any ideas ?


 >  sessionInfo()
R version 2.5.0 (2007-04-23)
x86_64-unknown-linux-gnu

locale:
C

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

other attached packages:
GEOquery
 "2.0.5"

and similarly :

 > sessionInfo()
R version 2.5.0 (2007-04-23)
i386-pc-mingw32

locale:
LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252

attached base packages:
 [1] "splines"   "grid"      "tools"     "stats"     "graphics"  
"grDevices" "utils"     "datasets"  "tcltk"     "methods"   "base"    

other attached packages:
     snapCGH         aCGH          sma     multtest      cluster         
GLAD          aws  tilingArray       pixmap  geneplotter
     "1.4.0"     "1.10.0"     "0.5.15"     "1.14.0"     "1.11.5"     
"1.10.0"      "1.3-2"     "1.14.0"      "0.4-7"     "1.14.0"
     lattice     annotate   genefilter     survival          vsn  
strucchange     sandwich          zoo RColorBrewer         affy
    "0.15-4"     "1.14.1"     "1.14.1"       "2.31"      "2.2.0"      
"1.3-2"      "2.0-2"      "1.3-1"      "0.2-3"     "1.14.0"
      affyio      Biobase        limma     GEOquery         svIO       
R2HTML       svMisc     svSocket        svIDE
     "1.4.0"     "1.14.0"     "2.10.0"      "2.0.5"      "0.9-5"       
"1.58"      "0.9-5"      "0.9-5"      "0.9-5"
 >


Sean Davis a écrit :
> On Friday 01 June 2007 09:16, Wolfgang Raffelsberger wrote:
>   
>> Dear list,
>>
>> I'm trying to see if one could use the getGEO function (GEOquery
>> package) to load files from other locations than GEO.
>> In particular I'd like to load data from a local directory (under Windows).
>> I see that getGEOfile() function passes the specific GEO url to
>> download.file, but I haven't been successful in changing this ...
>> Any suggestions ?
>>     
>
> Hi, Wolfgang.
>
> See the help for getGEO.  There is a filename argument that does exactly what 
> you are describing.  
>
> Sean
>
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>
>
>
>   


-- 

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 
. . .

Wolfgang Raffelsberger, PhD
Laboratoire de BioInformatique et Génomique Intégratives
IGBMC
1 rue Laurent Fries,  67404 Illkirch  Strasbourg,  France
Tel (+33) 388 65 3300         Fax (+33) 388 65 3276
http://www-bio3d-igbmc.u-strasbg.fr/~wraff
wolfgang.raffelsberger at igbmc.u-strasbg.fr