Re: getGEO error

On Thu, Jan 24, 2013 at 11:59 PM, Alyaa Mahmoud <alyamahmoud@...>wrote:

> Dear Group
>
> I am trying to download some datasets from GEO using package GEOquery. It
> worked fine for most of the datasets except for a couple of them, I get the
> following error:
> *
> *
> Error in read.table(file = file, header = header, sep = sep, quote = quote,
>  :
>   no lines available in input
> *
> *
> This is the script line I use:
> GSE3783 <-getGEO("GSE37830", GSEMatrix = TRUE)[[1]]
>
> I also tried to download the soft files and read these directly;
> GSE37830 = getGEO (filename = "GSE37830_family.soft.gz")
>
> but I still get the same error.
>
> Please advise
> Thanks a lot
>
> Alyaa Mahmoud
>

your version of R is very old -- current is 2.15.2; GEOquery has current
version 2.24.0.  There are many
changes that have occurred since 2009.  Please update (first R, then your
Bioconductor packages) and if further problems persist, file a new report.

>
> R version 2.9.2 (2009-08-24)
> x86_64-pc-linux-gnu
>
> locale:
>
> LC_CTYPE=C;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GEOquery_2.8.0 RCurl_1.95-3   bitops_1.0-5   Biobase_2.4.1
>
> loaded via a namespace (and not attached):
> [1] tools_2.9.2
>
> --
> Alyaa Mahmoud
>
> "Love all, trust a few, do wrong to none"- Shakespeare
>
>         [[alternative HTML version deleted]]
>
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