[BioC] GEOquery problem

[Sean Davis]

On Fri, Mar 19, 2010 at 10:35 AM, Ding, Wei <wei.ding at spcorp.com> wrote:
> Hi,
>
> I am trying to use getGEO function to get GEO data. It worked like charm
> before, howevre I can't get it working recently. The errors are not
> consistant. Sometimes I got error like
>> gse10240 <- getGEO("GSE2034", GSEMatrix=T)
> Error in curlPerform(curl = curl, .opts = opts, .encoding = .encoding) :
>
>  Access denied: 421
>
> Even after Sean mentioned it's solved

Hi, Wei.  This problem is not an issue with GEOquery, I do not think.
If you continue to have persistent problems with connections from your
location, please contact NCBI GEO.

> Most times I got the following error. It seems that I could download the
> the data, even with some warning message. However I couldn't open the
> data.
>> gse10240 <- getGEO("GSE10240", GSEMatrix=T)
> Found 1 file(s)
> GSE10240_series_matrix.txt.gz
> trying URL
> 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE10240/GSE10240_seri
> es_matrix.txt.gz'
> using Synchronous WinInet calls
> opened URL
> downloaded 1.1 Mb
>
> trying URL
> 'http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL571&form
> =text&view=full'
> Content type 'geo/text' length 200 bytes opened URL downloaded 27.5 Mb
>
> File stored at:
> C:\DOCUME~1\wding\LOCALS~1\Temp\RtmpqjnEHq/GPL571.soft
> Warning message:
> In download.file(myurl, destfile, mode = mode) :
>  downloaded length 28885636 != reported length 200
>> names(gse10240)
> [1] "GSE10240_series_matrix.txt.gz"
>> names(gse10240)
> [1] "GSE10240_series_matrix.txt.gz"
>
>> lapply(GSMList(gse10240), function(x) {Meta(x)$platform})
> Error in function (classes, fdef, mtable)  :
>  unable to find an inherited method for function "GSMList", for
> signature "list"

Using getGEO(...., GSEMatrix=TRUE) is the default.  The return from
getGEO, then, is a list of ExpressionSets.  In this case, try:

gse10240[[1]]

This is the first element of the returned list and since there is only
one Matrix file for GSE10240, this is the only element of that list.
If you need to know more about what an ExpressionSet is, please refer
to the Biobase documentation.

Hope that helps,
Sean

>
>
> Any idea?
>
> Wei
>
> ---------------------------------------
>
> Wei Ding, PhD
> Principal Scientist
> Molecular Design and Informatics
> T: 908 740 2592
> F: 908 740 4496
> wei.ding at spcorp.com
>
>
> Merck Research Laboratories
> 2015 Galloping Hill Road
> Kenilworth, NJ 07033 USA
> www.merck.com
>
>
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