[BioC] Import files from Applied Biosystems 7900HT?

Brian Diggs diggsb at ohsu.edu
Mon Apr 19 23:26:08 CEST 2010




Though I have used R for a few years, I am starting a project where this 
is my first real use of Bioconductor and I am having a problem reading 
expression data from files.  The files are created by an Applied 
Biosystems 7900HT machine.  I found the ABarray package, but that only 
claims to work with AB1700 data.  On a lark, I tried to use it for my 
data, but got an error

Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, 
na.strings,  :
   line 2 did not have 3 elements

which seems consistent with a file not being in the right format.  Can 
anyone tell me if there exists a package that can read this data into an 
ExpressionSet?  Or has anyone even used Bioconductor with data from 
this, and, if so, what needs to be done to import the data?

--
Brian Diggs
Senior Research Associate, Department of Surgery, Oregon Health & 
Science University



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