Question: GEOquery error
0
gravatar for Reema Singh
9.0 years ago by
Reema Singh570
Reema Singh570 wrote:
Hi All I am using GEOquery package to convert the dataset into expression set..But i m getting the following error.Here my script. library(Biobase) library(GEOquery) library(limma) gds <- getGEO(filename="/home/reemas/Desktop/GDS2821.soft.gz") eset <- GDS2eSet(gds,do.log2=TRUE) Error in download.file(myurl, destfile, mode = mode, quiet = TRUE) : cannot open URL ' ftp://ftp.ncbi.nih.gov/pub/geo/DATA/annotation/platforms/GPL570.annot. gz' Internet connection is there on my machine,then why its not connecting to ftp.. * REGRADS~ Reema Singh * [[alternative HTML version deleted]]
convert geoquery • 661 views
ADD COMMENTlink modified 9.0 years ago by Sean Davis21k • written 9.0 years ago by Reema Singh570
Answer: GEOquery error
0
gravatar for Dan Tenenbaum
9.0 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
On Mon, Dec 13, 2010 at 5:18 AM, Reema Singh <reema28sep@gmail.com> wrote: > Hi All > > I am using GEOquery package to convert the dataset into expression set..But > i m getting the following error.Here my script. > > library(Biobase) > library(GEOquery) > library(limma) > gds <- getGEO(filename="/home/reemas/Desktop/GDS2821.soft.gz") > eset <- GDS2eSet(gds,do.log2=TRUE) > > Error in download.file(myurl, destfile, mode = mode, quiet = TRUE) : > cannot open URL ' > ftp://ftp.ncbi.nih.gov/pub/geo/DATA/annotation/platforms/GPL570.anno t.gz' > > Internet connection is there on my machine,then why its not connecting to > ftp.. > > Hi Reema, Sometimes it appears the ftp server at NIH is not reliable. I suggest you try again. Dan > * > REGRADS~ > > Reema Singh > * > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 9.0 years ago by Dan Tenenbaum8.2k
Answer: GEOquery error
0
gravatar for Sean Davis
9.0 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
Hi, Reema. Try setting the download.file.method to curl: options("download.file.method"="curl") Sean On Dec 13, 2010 8:20 AM, "Reema Singh" <reema28sep@gmail.com> wrote: > Hi All > > I am using GEOquery package to convert the dataset into expression set..But > i m getting the following error.Here my script. > > library(Biobase) > library(GEOquery) > library(limma) > gds <- getGEO(filename="/home/reemas/Desktop/GDS2821.soft.gz") > eset <- GDS2eSet(gds,do.log2=TRUE) > > Error in download.file(myurl, destfile, mode = mode, quiet = TRUE) : > cannot open URL ' > ftp://ftp.ncbi.nih.gov/pub/geo/DATA/annotation/platforms/GPL570.anno t.gz' > > Internet connection is there on my machine,then why its not connecting to > ftp.. > > * > REGRADS~ > > Reema Singh > * > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD COMMENTlink written 9.0 years ago by Sean Davis21k
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