[BioC] GEOquery-Problem related to importing data set

[James W. MacDonald]

Hi Roopa,

On 9/10/2012 4:08 PM, Roopa Subbaiaih wrote:
> Hi All,
>
> I am trying to import few affy datasets into bioconductor.When I try the
> example given in R script it works fine but not the case with the dataset I
> need to import.
>
>   gds<-
> getGEO(filename=system.file("extdata/GDS2478.soft.gz",package="GEOquery"))

Unless you put the file there, I doubt you are pointing to the right 
place. Note that the vignette uses the extdata directory for data that 
come with the GEOquery package - that isn't where you should put things.

Here is what I got:

 > getGEO("GDS2478")
File stored at:
C:\Users\BIOINF~1\AppData\Local\Temp\RtmpYDVgJB/GDS2478.soft.gz
 > dat <- 
getGEO(filename="C:/Users/BIOINF~1/AppData/Local/Temp/RtmpYDVgJB/GDS2478.soft.gz")
 > class(dat)
[1] "GDS"
attr(,"package")
[1] "GEOquery"

And to see what is in a GDS object,

?GDS-class
and
?GEOData-class

and from there I get

 > head(Table(dat))
      ID_REF IDENTIFIER GSM148887 GSM148888 GSM148889 GSM148890 GSM148892
1 1007_s_at       DDR1   760.999   754.827   758.415   746.281   776.563
2   1053_at       RFC2    93.978    113.67    110.74   114.423   140.641
3    117_at      HSPA6    39.268    40.784    42.345    37.779    44.122
4    121_at       PAX8    189.36   194.713   208.084   180.112    223.06
5 1255_g_at     GUCA1A    11.864     8.857    10.754     9.224    10.396
6   1294_at       UBA7    70.985    78.527    79.646    70.705    77.107

Best,

Jim



> 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
> This what i get.
>
> Please let me know how to rectify this. Thanks, Roopa
>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099