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/GSM528276.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//GSM528276.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

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