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 > ??URL?ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE462/GSE462 _series_matrix.txt.gz' > ftp?data?connection?made,?file?length?171874?bytes > ???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) > ???function?(classes,?fdef,?mtable)??: > ??unable?to?find?an?inherited?method?for?function?"Meta",?for?signat ure?"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)) > ???function?(classes,?fdef,?mtable)??: > ??unable?to?find?an?inherited?method?for?function?"GSMList",?for?sig nature?"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