[BioC] Import files from Applied Biosystems 7900HT?

[Michael Muratet]

On Apr 22, 2010, at 3:50 PM, Heidi Dvinge wrote:

>> 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.
>>
> Hello Brian,
>
> ExpressionSet objects (and the packages that use them) are  
> specifically
> designed for microarray data. So if you have qPCR data you're better  
> of
> using HTqPCR or some other package designed for qPCR.
>
> It looks like you have standard SDS format. In that case you don't  
> need to
> do any conversions to read the data into HTqPCR. If you have the  
> latest
> version, 1.1.4, there's a parameter called "SDS" in readCtData. If  
> you set
> that to TRUE it should work.
Hi guys

I would check and make sure you have a Ct column in the data. Some SDS  
export settings will produce it (i.e., the plate-centric view) and  
some won't in favor of ddCt and RQ. The header data shows up in them  
all.

Mike

>
> HTH
> \Heidi
>
>>>>
>>>> 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
>>
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>
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Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

Room 4005
601 Genome Way
Huntsville, Alabama 35806