[BioC] GEOquery-Problem related to importing data set

[James W. MacDonald]

Hi Roopa,

On 9/10/2012 4:50 PM, Roopa Subbaiaih wrote:
> Thank you very much. I tried to follow what you did.This is what I get.
>  getGEO("GDS2478")
> Error in download.file(myurl, destfile, mode = mode, quiet = TRUE, 
> method = getOption("download.file.method.GEOquery")) :
>   cannot open URL 
> 'ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/SOFT/GDS/GDS2478.soft.gz'
> Am I missing something?

Well, there is the obvious - you are connected to the internet, yes? If 
so, does the following code download some data?

  read.table("ftp://ftp.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat")

if not, does this help (here I am assuming you are on Windows)?

setInternet2(NA)
read.table("ftp://ftp.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat")

If so, you should then be able to use getGEO().

Best,

Jim


> Thank you for the quick response. Roopa
>
>
> On Mon, Sep 10, 2012 at 4:33 PM, James W. MacDonald <jmacdon at uw.edu 
> <mailto:jmacdon at uw.edu>> wrote:
>
>     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
>
>
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099