Hi, I would like to re-analyse some array files which are in the GEO repository. These are illumina bead array expression data. Once I have downloaded the GSM file, is there a pacakge I can use that can handle these data? I look for basic information on the detection levels ( like the BeadStudio software)? I saw the beadarray pacakge which has a lot of function, has somebody some experience with this package and could give me some advise on how to get these basic data? many thanks Nathalie -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

On Tue, Jun 14, 2011 at 10:34 AM, nac <nac at="" sanger.ac.uk=""> wrote: > Hi, > I would like to re-analyse some array files which are in the GEO > repository. These are illumina bead array expression data. Once I have > downloaded the GSM file, is there a pacakge I can use that can handle these > data? I look for basic information on the detection levels ( like the > BeadStudio software)? I saw the beadarray pacakge which has a lot of > function, has somebody some experience with this package and could give me > some advise on how to get these basic data? > many thanks Hi, Natalie. You'll need to look at the files available from GEO. There may be a supplemental file that is in a format that beadarray understands. Alternatively, you could get the data using the GEOquery package and extract the information you need from the GEO files. Unfortunately, it will be up to you to figure out what information GEO provides. If you need a bit more help, you could try sending the GEO accessions to the list and perhaps someone can help you determine what file formats are available and how they might best be handled. Sean