[BioC] error with getGEO;ask for help

[Sean Davis]

2009/12/18 ruansun <ruansun at 163.com>:
> Dear Dr. Davis
>        I am a user of your R package GEOquery. I ran into some problems when
> I tried to import GSE data with the getGEO function.
>
> For example
>> gse462=getGEO("GSE462",destdir="d:\\datas")
> Found 1 file(s)
> GSE462_series_matrix.txt.gz
> 试开URL’ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE462/GSE462_series_matrix.txt.gz'
> ftp data connection made, file length 171874 bytes
> 打开了URL
> downloaded 167 Kb
> File stored at:
> C:\DOCUME~1\happy\LOCALS~1\Temp\RtmpCu25Ed/GPL5.soft

gse462 is a list of length 1.

class(gse462)
length(gse462)

And each member of the list is an ExpressionSet.

class(gse462[[1]])


>> Meta(gse462)
> 错误于function (classes, fdef, mtable)  :
>   unable to find an inherited method for function "Meta", for signature "list"

The new default (for about a year) is to use GSEMatrix=TRUE when
getting GSE data.  This will return a list of ExpressionSets and not a
GSE object.  Meta() is for use with GSE objects and not with
ExpressionSets.

>> names(GSMList(gse462))
> 错误于function (classes, fdef, mtable)  :
>   unable to find an inherited method for function "GSMList", for signature "list"

Do something like:

gse462eSet = gse462[[1]]

gse462eSet is now simply an ExpressionSet.  You can read about
ExpressionSets in the Biobase Vignettes and also in the help pages.

Sorry for the confusion about the two different ways of getting GSE
data.  I hope this clears things up a bit.  If not, please ask.

Sean