[BioC] Import files from Applied Biosystems 7900HT?

[Brian Diggs]

On 4/21/2010 2:38 PM, Michael Muratet wrote:
>
> 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

Thank you for the information, Heidi and Mike, especially given how 
vague I was.  The data is from Taqman Low Density Arrays and is qPCR data.

I am not doing the runs myself, though I have access to the person who 
is.  We are still working out details in workflow.  The files I have 
been getting thus far are, I think, SDS files.  They have a .txt 
extension, but the first few lines are:

SDS 2.3	AQ Results	1.0
Filename	TLDA-M10-21T_ALL cDNA042110
PlateID	
Assay Type	Absolute Quantification
Run DateTime	4/21/10 1:28:40 PM

I don't have a copy of the RQ manager software myself, but I know it is 
on the computer running the machine.  I'll see about getting a copy of 
it for myself or getting some time to do the conversion on the original 
computer and see about importing the data using HTqPCR::readCtData then.

>>
>> 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
>>>
>
> Michael Muratet, Ph.D.
> Senior Scientist
> HudsonAlpha Institute for Biotechnology
> mmuratet-Sy0TgEBENMiWTJ9x5QRIJA at public.gmane.org
> (256) 327-0473 (p)
> (256) 327-0966 (f)
>
> Room 4005
> 601 Genome Way
> Huntsville, Alabama 35806
>

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