I am using windows XP 32 bit. I tried your suggestion and this is what I
get-

> setInternet2(NA)
[1] FALSE
> read.table("ftp://ftp.stats.ox.ac.uk/pub/datasets/csb/ch11b.dat")
Error in file(file, "rt") : cannot open the connection
I am fairly new to R.

Please let me know if I can try any other option.

Thank you, Roopa

On Mon, Sep 10, 2012 at 5:04 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> 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<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<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<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@uw.edu<mailto:
>> jmacdon@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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>>         Bioconductor@r-project.org <mailto:Bioconductor@r-**project.org<Bioconductor@r-project.org>>
>>
>>
>>         https://stat.ethz.ch/mailman/**listinfo/bioconductor<https://stat.ethz.ch/mailman/listinfo/bioconductor>
>>         Search the archives:
>>         http://news.gmane.org/gmane.**science.biology.informatics.**
>> conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor>
>>
>>
>>     --     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
>
>


-- 
---------------------------------------
Roopa Shree Subbaiaih
Post Doctoral Fellow
Department of Orthopaedics
School of Medicine
Case Western Reserve University
Cleveland, OH-44106
Tel:+1 216 368 1380

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