[Bioc-devel] GEOquery Warnings When Reading SOFT File

James W. MacDonald jmacdon at uw.edu
Thu Feb 19 15:48:19 CET 2015


Hi Dario,

This isn't the right forum for your question (this listserv is for
development of packages, not questions about existing packages), so you
should ask on the support site.

Best,

Jim



On Thu, Feb 19, 2015 at 1:00 AM, Dario Strbenac <dstr7320 at uni.sydney.edu.au>
wrote:

> library(GEOquery)
> gastricChina <- getGEO("GSE65801", GSEMatrix = FALSE)
>
> Generates warnings
>
> > head(warnings(), 1)
> Warning message:
> In readLines(con, n = chunksize) :
>   seek on a gzfile connection returned an internal error
>
> Does it affect the correctness of the imported data ?
>
> Also, experimentData(gastricChina) gives an empty result
>
> Experiment data
>   Experimenter name:
>   Laboratory:
>   Contact information:
>   Title:
>   URL:
>   PMIDs:
>   No abstract available.
>
> whereas some of the fields are filled in on the webpage.
>
> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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