Hello, For a particular GSE set I have downloaded all the raw data but I would like to be able to extract all the phenodata associated with each sample into a table so I can use it in the analysis. 4.1 of the manual shows a way of getting what I want but I would have to download the whole GSE matrix. Is there a way of getting just the meta data? Thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}

On Tue, Oct 26, 2010 at 5:38 AM, Daniel Brewer <daniel.brewer@icr.ac.uk>wrote: > Hello, > > For a particular GSE set I have downloaded all the raw data but I would > like to be able to extract all the phenodata associated with each sample > into a table so I can use it in the analysis. 4.1 of the manual shows a > way of getting what I want but I would have to download the whole GSE > matrix. Is there a way of getting just the meta data? > > Hi, Dan. The best way is to use getGEO() on the GSE and then extract the phenoData object from that. I know that means downloading the entire GSE Matrix file since partial GSE Matrix files are not available. I had toyed with getting partial SOFT format output early on in GEOquery development, but I didn't complete that work as it required working with the web form and that felt a little unsafe for maintenance. Note that a few GSEs are now including separate data tables with the sample annotation. These can be downloaded using the getGSEDataTables() function. Sean [[alternative HTML version deleted]]