How to extract Phenotype data from GSE
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Reema Singh ▴ 570
@reema-singh-4373
Last seen 7.0 years ago
HI Gaurav Have you solved your problem?. I am also facing the same problem. I did it as James mention,but still i m not able to get phenotypic information. Here is the steps:- gse <- getGEO(filename='GPL10265/GSE21111_family.soft.gz',GSEMatrix=TRUE) pData(gse[[1]]) OR phenoData(gse[[1]]) Error in pData(gse[[1]]) : error in evaluating the argument 'object' in selecting a method for function 'pData': Error in gse[[1]] : this S4 class is not subsettable Thanx On Thu, May 19, 2011 at 1:32 PM, James F. Reid < james.reid@ifom-ieo-campus.it> wrote: > 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 >> >> >> > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > [[alternative HTML version deleted]]
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James F. Reid ▴ 610
@james-f-reid-3148
Last seen 7.0 years ago
Hi Reema, On 07/11/11 03:34, Reema Singh wrote: > HI Gaurav > > Have you solved your problem?. I am also facing the same problem. I did > it as James mention,but still i m not able to get phenotypic > information. Here is the steps:- > > gse <- getGEO(filename='GPL10265/GSE21111_family.soft.gz',GSEMatrix=TRUE) > pData(gse[[1]]) OR phenoData(gse[[1]]) > Error in pData(gse[[1]]) : > error in evaluating the argument 'object' in selecting a method for > function 'pData': Error in gse[[1]] : this S4 class is not subsettable > > Thanx the reason this approach is not working for you is because you are using the SOFT file instead of the GSE_MATRIX. With the file 'GSE21111_series_matrix.txt.gz' the function getGEO will return a list of ExpressionSet(s) which you can query for phenotypic data using pData or phenoData. It would be easier to simply use: gse <- getGEO("GSE21111") Best, J. > > > On Thu, May 19, 2011 at 1:32 PM, James F. Reid > <james.reid at="" ifom-ieo-campus.it="" <mailto:james.reid="" at="" ifom-ieo-="" campus.it="">> > wrote: > > 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_ma trix.__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 > > > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > >
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