Question

Importing "Detailed sample annotation" from ArrayExpress DB into R

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Markus Schmidberger ▴ 380

@markus-schmidberger-2240

Last seen 10.2 years ago

Hello, I am looking for a function or package to import the "Detailed sample annotation" file from the ArrayExpress Database. For GEO there is the "GEOquery" package. For ArrayExpress there is the "ArraExpress" package. But I am looking for a function to import or read the "xxxxxx.sdrf.txt" file. Is there something? Thanks Markus -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://ibe.web.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de Tel: +49 (089) 7095 - 4599

ArrayExpress ArrayExpress • 1.6k views

ADD COMMENT • link 16.3 years ago • updated 16.2 years ago Markus Schmidberger ▴ 380

score 0 · Answer 1 · 2008-08-27

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Markus Schmidberger ▴ 380

@markus-schmidberger-2240

Last seen 10.2 years ago

Hi, I found a working solution: an <-read.table("E-GEOD-635.sdrf.txt", header=TRUE, sep="\t") Best Markus Markus Schmidberger schrieb: > Hello, > > I am looking for a function or package to import the "Detailed sample > annotation" file from the ArrayExpress Database. > For GEO there is the "GEOquery" package. For ArrayExpress there is the > "ArraExpress" package. > > But I am looking for a function to import or read the > "xxxxxx.sdrf.txt" file. Is there something? > > Thanks > Markus > -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://ibe.web.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de Tel: +49 (089) 7095 - 4599

ADD COMMENT • link 16.2 years ago Markus Schmidberger ▴ 380

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Hi Markus, This is effectively working. Another alternative is that the sdrf.txt file content is fully contained in the phenoData of the object created by the use of the ArrayExpress function from the ArrayExpress package. Best regards, Audrey Markus Schmidberger wrote: > Hi, > > I found a working solution: > an <-read.table("E-GEOD-635.sdrf.txt", header=TRUE, sep="\t") > > Best > Markus > > Markus Schmidberger schrieb: >> Hello, >> >> I am looking for a function or package to import the "Detailed sample >> annotation" file from the ArrayExpress Database. >> For GEO there is the "GEOquery" package. For ArrayExpress there is >> the "ArraExpress" package. >> >> But I am looking for a function to import or read the >> "xxxxxx.sdrf.txt" file. Is there something? >> >> Thanks >> Markus >> > > -- Audrey Kauffmann EMBL - EBI Cambridge UK http://www.ebi.ac.uk/~audrey

ADD REPLY • link 16.2 years ago audrey ▴ 280