Got it. Looks like the firewall in our department was creating trouble. Thanks for your patience. Roopa On Mon, Sep 10, 2012 at 5:17 PM, Roopa Subbaiaih <rss115@case.edu> wrote: > 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.da t<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]] >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> 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 > > -- --------------------------------------- Roopa Shree Subbaiaih Post Doctoral Fellow Department of Orthopaedics School of Medicine Case Western Reserve University Cleveland, OH-44106 Tel:+1 216 368 1380 [[alternative HTML version deleted]]