[BioC] Import files from Applied Biosystems 7900HT?

[Heidi Dvinge]

> 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.

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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