[BioC] Import files from Applied Biosystems 7900HT?

[Heidi Dvinge]

Hello Brian,

wait, is your data from a microarray or a qPCR plate? I think the 7900HT
machine is what Applied Biosystems use with the TaqMan Low Density Cards.
If so, you can use the package HTqPCR for reading in an processing the
data. The basic data structure there is a qPCRSet object, which is similar
to ExpressionSet, only designed for qPCR data.

If my memory is failing my regarding the 7900HT and you actually have
microarray data, then you should be able to read them into R using e.g.
the package limma.

HTH
\Heidi
>
>
>
> 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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