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Question: ddCt isn't working with exported ABI7500-RT-PACR file
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gravatar for Alnaji, Fadi
7.0 years ago by
Alnaji, Fadi20
Alnaji, Fadi20 wrote:
Hello I am trying to use the ddCt package which was developed by Jitao David Zhang, Rudolf Biczok and Markus Ruschhaupt. My problem is that it seems the package is not able to read the exported file, the one contains the individual ct Values, from ABI 7500 RT-PCR instrument. When I execute the package, it says your file is not .SDM. That's true, as my file is SDS, but this is the only possibility I have got in the machine. However I tried to play a bit with the text format in excel to make SDS as similar as the SDM in the package-example file. It worked indeed, but it is not a practical way I believe. Is there any other option to make this package able to read my SDS files, or to convert this file to SDM. Many thanks. [[alternative HTML version deleted]]
ADD COMMENTlink modified 7.0 years ago by james perkins300 • written 7.0 years ago by Alnaji, Fadi20
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gravatar for james perkins
7.0 years ago by
james perkins300
james perkins300 wrote:
Hey, You could try ReadqPCR or HTqPCR, both enable you to read in SDS files I believe (ReadqPCR has a read.qPCR function, and there is an explanation of how to do so in HTqPCR). If you were to have problems using your version of SDS file with ReadqPCR, I would be very grateful if you could email me your file (annonymsed if you wish of course) so I can alter ReadqPCR appropriately. Cheers, Jim On 1 December 2011 10:51, Alnaji, Fadi <f.alnaji at="" warwick.ac.uk=""> wrote: > > Hello > > I am trying to use the ddCt package which was developed by Jitao David > Zhang, Rudolf Biczok and Markus Ruschhaupt. My problem is that it seems > the package is not able to read the exported file, the one contains the > individual ct Values, from ABI 7500 RT-PCR instrument. When I execute > the package, it says your file is not .SDM. That's true, as my file is > SDS, but this is the only possibility I have got in the machine. However > I tried to play a bit with the text format in excel to make SDS as > similar as the SDM in the package-example file. It worked indeed, but it > is not a practical way I believe. > > Is there any other option to make this package able to read my SDS > files, or to convert this file to SDM. > > Many thanks. > > > > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 7.0 years ago by james perkins300
Deam Jim, thanks a lot. I'll try this out and let you know. All the best - Fadi -----Original Message----- From: jimrperkins@gmail.com [mailto:jimrperkins@gmail.com] On Behalf Of James Perkins Sent: 01 December 2011 11:42 To: Alnaji, Fadi Cc: bioconductor at r-project.org Subject: Re: [BioC] ddCt isn't working with exported ABI7500-RT-PACR file Hey, You could try ReadqPCR or HTqPCR, both enable you to read in SDS files I believe (ReadqPCR has a read.qPCR function, and there is an explanation of how to do so in HTqPCR). If you were to have problems using your version of SDS file with ReadqPCR, I would be very grateful if you could email me your file (annonymsed if you wish of course) so I can alter ReadqPCR appropriately. Cheers, Jim On 1 December 2011 10:51, Alnaji, Fadi <f.alnaji at="" warwick.ac.uk=""> wrote: > > Hello > > I am trying to use the ddCt package which was developed by Jitao David > Zhang, Rudolf Biczok and Markus Ruschhaupt. My problem is that it seems > the package is not able to read the exported file, the one contains the > individual ct Values, from ABI 7500 RT-PCR instrument. When I execute > the package, it says your file is not .SDM. That's true, as my file is > SDS, but this is the only possibility I have got in the machine. However > I tried to play a bit with the text format in excel to make SDS as > similar as the SDM in the package-example file. It worked indeed, but it > is not a practical way I believe. > > Is there any other option to make this package able to read my SDS > files, or to convert this file to SDM. > > Many thanks. > > > > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 7.0 years ago by Alnaji, Fadi20
Hi dear Fadi, The ddCt package currently only supports SDS format converted to TXT file format. HTqPCR should do the job - we will consider implementing the functionality in ddCt as well. Best wishes, David 2011/12/1 Alnaji, Fadi <f.alnaji@warwick.ac.uk> > Deam Jim, thanks a lot. > > I'll try this out and let you know. > > All the best - Fadi > > -----Original Message----- > From: jimrperkins@gmail.com [mailto:jimrperkins@gmail.com] On Behalf Of > James Perkins > Sent: 01 December 2011 11:42 > To: Alnaji, Fadi > Cc: bioconductor@r-project.org > Subject: Re: [BioC] ddCt isn't working with exported ABI7500-RT-PACR file > > Hey, > > You could try ReadqPCR or HTqPCR, both enable you to read in SDS files > I believe (ReadqPCR has a read.qPCR function, and there is an > explanation of how to do so in HTqPCR). If you were to have problems > using your version of SDS file with ReadqPCR, I would be very grateful > if you could email me your file (annonymsed if you wish of course) so > I can alter ReadqPCR appropriately. > > Cheers, > > Jim > > On 1 December 2011 10:51, Alnaji, Fadi <f.alnaji@warwick.ac.uk> wrote: > > > > Hello > > > > I am trying to use the ddCt package which was developed by Jitao David > > Zhang, Rudolf Biczok and Markus Ruschhaupt. My problem is that it seems > > the package is not able to read the exported file, the one contains the > > individual ct Values, from ABI 7500 RT-PCR instrument. When I execute > > the package, it says your file is not .SDM. That's true, as my file is > > SDS, but this is the only possibility I have got in the machine. However > > I tried to play a bit with the text format in excel to make SDS as > > similar as the SDM in the package-example file. It worked indeed, but it > > is not a practical way I believe. > > > > Is there any other option to make this package able to read my SDS > > files, or to convert this file to SDM. > > > > Many thanks. > > > > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Jitao David Zhang Computational Biologist http://www.NextBioMotif.com/ [[alternative HTML version deleted]]
ADD REPLYlink written 7.0 years ago by Jitao David Zhang340
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