[BioC] Import files from Applied Biosystems 7900HT?

[Michael Muratet]

On Apr 21, 2010, at 2:54 PM, Heidi Dvinge wrote:

> 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.

Greetings

Having just gone through a similar process, I found it depends a lot  
on how the data were processed by the SDS software if you have 7900HT  
data. Do you have the original *.sds files, or *.sdm or some other  
format? I read the original *.sds files into the RQ manager software,  
set the window to be 'Plate Centric' and then I could export 'Results'  
and the files had the format expected by HTqPCR. These were not the  
settings I got when I first started the software and it took some  
trial and error to figure it out.

Cheers

Mike

>
> 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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>
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Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
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