Hi guys, I tried to use GEOquery to retrieve raw file, but got "No supplemental files found". > a <- getGEOSuppFiles("GSM528276", makeDirectory = TRUE, baseDir = getwd()) [1] "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528276/suppl/" No supplemental files found > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US [4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US [7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GEOquery_2.28.0 Biobase_2.22.0 BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] RCurl_1.95-4.1 XML_3.98-1.1 > The direct address for the raw file is ftp://ftp.ncbi.nlm.nih.gov/geo/ samples/GSM528nnn/GSM528276/suppl/GSM528276.CEL.gz. Any suggestion? Thanks a lot! Ying Confidentiality Note:\ This e-mail, and any attachment t...{{dropped:11}}

On Thu, Feb 13, 2014 at 5:05 PM, Ying Chen <ying.chen@imclone.com> wrote: > Hi guys, > > I tried to use GEOquery to retrieve raw file, but got "No supplemental > files found". > > > a <- getGEOSuppFiles("GSM528276", makeDirectory = TRUE, baseDir > = getwd()) > [1] " > ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528276/suppl/" > No supplemental files found > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US > [4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US > [7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets > methods > [8] base > > other attached packages: > [1] GEOquery_2.28.0 Biobase_2.22.0 BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.95-4.1 XML_3.98-1.1 > > > > The direct address for the raw file is > ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528276/suppl/GSM 528276.CEL.gz > . > Hi, Ying. This works for me, so you might try again. Network connectivity and ftp changes have been known to affect this before. Sean > a <- getGEOSuppFiles("GSM528276", makeDirectory = TRUE, baseDir = getwd()) [1] "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528276/suppl/" trying URL ' ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM528nnn/GSM528276/suppl//GSM5 28276.CEL.gz ' ftp data connection made, file length 3598293 bytes opened URL ================================================== downloaded 3.4 Mb > sessionInfo() R version 3.0.2 Patched (2014-01-22 r64855) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GEOquery_2.28.0 Biobase_2.21.7 BiocGenerics_0.7.5 [4] BiocInstaller_1.12.0 loaded via a namespace (and not attached): [1] RCurl_1.95-4.1 XML_3.95-0.2 [[alternative HTML version deleted]]