ddCt isn't working with exported ABI7500-RT-PACR file

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Alnaji, Fadi ▴ 20

@alnaji-fadi-4985

Last seen 10.2 years ago

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]]

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ADD COMMENT • link updated 13.0 years ago by james perkins ▴ 300 • written 13.0 years ago by Alnaji, Fadi ▴ 20

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james perkins ▴ 300

@james-perkins-2675

Last seen 10.2 years ago

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 COMMENT • link 13.0 years ago james perkins ▴ 300

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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 REPLY • link 13.0 years ago Alnaji, Fadi ▴ 20

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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 REPLY • link 13.0 years ago Jitao David Zhang ▴ 340

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