[BioC] Import files from Applied Biosystems 7900HT?

Thu Apr 22 23:20:38 CEST 2010

On 4/22/2010 2:08 PM, Michael Muratet wrote:
>
> 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

My files do have a Ct column, so that is promising.  I had seen the SDS 
flag in readCtData, but it did not work even with that.  However, I now 
realize that I have version 1.0 of HTqPCR, probably because I am still 
on (the as of today no longer current) R 2.10.1 and Bioconductor 2.5. 
I'm going to wait for the new R 2.11.0 binaries to propagate to my local 
mirror and for the release of Bioconductor 2.6 (which I understand 
happens a few days after a release of R) so that I don't have switch to 
the development versions just to get the latest HTqPCR.

I'll see if I can import the data directly without any further 
manipulations after the update.  Thank you both for your help.

>>
>> 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-XMD5yJDbdMReXY1tMh2IBg 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-Sy0TgEBENMiWTJ9x5QRIJA at public.gmane.org
> (256) 327-0473 (p)
> (256) 327-0966 (f)
>
> Room 4005
> 601 Genome Way
> Huntsville, Alabama 35806
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor-J/1JLT8/XkkyrOtl8ohm9u1GAupnlqi7 at public.gmane.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

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