Dear Sean and bioconductor users, I?m new to GEOquery and things are not very clear to me as my understanding is limited for the package. I need to know phenotypic data for GSE3149. After reading GEOquery manual and mail-archive. I did following to find the Phenotypic information for GSE3149. >gse3149<-getGEO(filename='D:/GSE3149/GSE3149_series_matrix.txt.gz', GSEMatrix=TRUE) >phenotype <- pData(phenoData(gse3149[[1]])) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "phenoData", for signature "factor" Error in pData(phenoData(gse3149[[1]])) : error in evaluating the argument 'object' in selecting a method for function 'pData' However, I can see phenoData through show function (> show(gse3149)) Please, guide me where i?m doing wrong. Thanks in advance Gaurav -- ---------------------- PhD Student (Bioinformatics/Computational Biology) Prof. Shoba Ranganathan Lab Dept. of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, Australia. URL:http://gauravkumar.org

Hi Gaurav, just use phenoData(gse3149[[1]]) to get an 'AnnotatedDataFrame' or pData(gse3149[[1]]) to get a data.frame. HTH. J. On 05/19/2011 08:36 AM, Gaurav Kumar wrote: > Dear Sean and bioconductor users, > > I?m new to GEOquery and things are not very clear to me as my > understanding is limited for the package. I need to know phenotypic > data for GSE3149. After reading GEOquery manual and mail-archive. I > did following to find the Phenotypic information for GSE3149. > >> gse3149<-getGEO(filename='D:/GSE3149/GSE3149_series_matrix.txt.gz', GSEMatrix=TRUE) > >> phenotype<- pData(phenoData(gse3149[[1]])) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "phenoData", for > signature "factor" > Error in pData(phenoData(gse3149[[1]])) : > error in evaluating the argument 'object' in selecting a method for > function 'pData' > > However, I can see phenoData through show function (> show(gse3149)) > > Please, guide me where i?m doing wrong. > Thanks in advance > Gaurav > >