[BioC] GEOquery

[Zhu, Julie]

With sessionInfo() this time. Thanks!

Julie

On 3/31/10 6:07 PM, "Julie Zhu" <julie.zhu at umassmed.edu> wrote:

> Hi,
> 
> First of all I would like to thank the developers for developing such a useful
> package!
> 
> I downloaded a dataset using GEOquery package successfully as following.
> However, I could not convert it to eSet or get metadata out of it. Could you
> please let me know what I did wrong and how to proceed? Thanks so much for
> your help!
> 
> Best regards,
> 
> Julie
> 
>> gds <- getGEO('GSE6547')
> Found 1 file(s)
> GSE6547_series_matrix.txt.gz
> trying URL 
> 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE6547/GSE6547_series_matri
> x.txt.gz'
> ftp data connection made, file length 1739964 bytes
> opened URL
> ==================================================
> downloaded 1.7 Mb
> 
> File stored at: 
> /tmp/RtmpaOAhXo/GPL200.soft
> 
>> eset <- GDS2eSet(gds, do.log2 = TRUE)
> Error in function (classes, fdef, mtable)  :
>   unable to find an inherited method for function "Meta", for signature "list"
> 
>> Meta(gds)
> Error in function (classes, fdef, mtable)  :
>   unable to find an inherited method for function "Meta", for signature "list"
>> Table(gds)
> Error in function (classes, fdef, mtable)  :
>   unable to find an inherited method for function "Table", for signature
> "list"
>> Columns(gds)
> Error in function (classes, fdef, mtable)  :
>   unable to find an inherited method for function "Columns", for signature
> "list"

Here is the sessionInfo

> sessionInfo()
R version 2.10.1 (2009-12-14)
i386-apple-darwin8.11.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] GEOquery_2.11.3                     RCurl_1.3-1
 [3] bitops_1.0-4.1                      ChIPpeakAnno_1.2.13
 [5] limma_3.2.3                         org.Hs.eg.db_2.3.6
 [7] GO.db_2.3.5                         RSQLite_0.8-2
 [9] DBI_0.2-5                           AnnotationDbi_1.8.2
[11] BSgenome.Ecoli.NCBI.20080805_1.3.16 BSgenome_1.14.2
[13] Biostrings_2.14.12                  IRanges_1.4.16
[15] multtest_2.2.0                      Biobase_2.6.1
[17] biomaRt_2.2.0 

loaded via a namespace (and not attached):
[1] MASS_7.3-4      splines_2.10.1  survival_2.35-7 tools_2.10.1
XML_2.6-0      


*******************************************
Lihua Julie Zhu, Ph.D
Research Associate Professor
Program Gene Function and Expression
University of Massachusetts Medical School
364 Plantation Street, Room 613
Worcester, MA 01605
508-856-5256
http://www.umassmed.edu/pgfe/faculty/zhu.cfm