loading AB OpenArray qPCR data in HTqPCR
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Guido Hooiveld ★ 3.4k
@guido-hooiveld-2020
Last seen 2 days ago
Wageningen University, Wageningen, the …
Dear Heidi & list, I was given the output from an miRNA screening experiment performed on the mouse TaqMan OpenArray microRNA panel from Applied Biosystems (formerly Biotrove). This is a microfluidic card / slide, on which 3 samples can be simultaneously screened for mouse miRNAs. https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavi gate2&catID=608441&tab=DetailInfo Since I have understood HTqPCR is compatible with most Applied output files, and i read in the vignette that Fluidigm microfluidics data can be imported in HTqPCR, I wondered whether HTqPCR also could be used to import and analyse OpenArray datasets, or whether you (or someone else) could recommend another package for processing. I do have data available in *.ncx format (also exported as .csv), but i have to admit i don't fully understand the content of all columns... Regards, Guido --------------------------------------------------------- Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld@wur.nl internet: http://nutrigene.4t.com http://www.researcherid.com/rid/F-4912-2010 [[alternative HTML version deleted]]
miRNA microRNA HTqPCR miRNA microRNA HTqPCR • 888 views
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Heidi Dvinge ★ 2.0k
@heidi-dvinge-2195
Last seen 8.1 years ago
Hi Guido, > Dear Heidi & list, > > I was given the output from an miRNA screening experiment performed on the > mouse TaqMan OpenArray microRNA panel from Applied Biosystems (formerly > Biotrove). This is a microfluidic card / slide, on which 3 samples can be > simultaneously screened for mouse miRNAs. > https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNa vigate2&catID=608441&tab=DetailInfo > > Since I have understood HTqPCR is compatible with most Applied output > files, and i read in the vignette that Fluidigm microfluidics data can be > imported in HTqPCR, I wondered whether HTqPCR also could be used to import > and analyse OpenArray datasets, or whether you (or someone else) could > recommend another package for processing. > I do have data available in *.ncx format (also exported as .csv), but i > have to admit i don't fully understand the content of all columns... > I haven't come across OpenArray data sets before, so there's no default way for loading them into HTqPCR. However, in principle all that's required is a qPCR probe or gene ID and a corresponding Ct value, in some format that can be read by R (such as comma or tab separated values). I'll be fixing some issues in HTqPCR soon in advance of the coming Bioconductor October release. Hence, if there's any other requests for additions to HTqPCR I might as well do that as the same time. In order to add new input data formats I need someone willing to let me have some test data tho'. This can of course be anonymised/randomised as desired. Cheers \Heidi > Regards, > Guido > > > > --------------------------------------------------------- > Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > email: guido.hooiveld at wur.nl > internet: http://nutrigene.4t.com > http://www.researcherid.com/rid/F-4912-2010 > > > [[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 >
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