Openening qPCR file from ABI
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Guest User ★ 13k
@guest-user-4897
Last seen 9.6 years ago
Hi, a colleague of mine gave me a 'sds' file, containing Real-Time PCR data from an ABI machine. I am currently trying to open it using the "ReadqPCR" package, but I am getting errors using it. So maybe someone knows another package/way which I could go to open this file? Best, Philippe -- output of sessionInfo(): R version 2.15.0 (2012-03-30) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ReadqPCR_1.2.0 affy_1.34.0 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affyio_1.24.0 BiocInstaller_1.4.7 preprocessCore_1.18.0 [4] zlibbioc_1.2.0 -- Sent via the guest posting facility at bioconductor.org.
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Matthias Kohl ▴ 160
@matthias-kohl-1678
Last seen 9.6 years ago
Dear Philippe, without the R code you've used, it is hard to say what has caused the errors. Which errors? Best, Matthias On 09.08.2012 06:06, Philippe [guest] wrote: > > Hi, > > a colleague of mine gave me a 'sds' file, containing Real-Time PCR data from an ABI machine. I am currently trying to open it using the "ReadqPCR" package, but I am getting errors using it. So maybe someone knows another package/way which I could go to open this file? > > Best, > Philippe > > -- output of sessionInfo(): > > R version 2.15.0 (2012-03-30) > Platform: i686-pc-linux-gnu (32-bit) > > locale: > [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C > [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 > [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ReadqPCR_1.2.0 affy_1.34.0 Biobase_2.16.0 BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] affyio_1.24.0 BiocInstaller_1.4.7 preprocessCore_1.18.0 > [4] zlibbioc_1.2.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 > -- Prof. Dr. Matthias Kohl www.stamats.de
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Guido Hooiveld ★ 3.9k
@guido-hooiveld-2020
Last seen 1 day ago
Wageningen University, Wageningen, the …
Hi Philippe, If i recall correctly the package HTqPCR should be able to open ABI's SDS files. See chapter 13.1, page 43 of the manual. http://www.bioconductor.org/packages/2.10/bioc/html/HTqPCR.html HTH, 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://scholar.google.com/citations?user=qFHaMnoAAAAJ http://www.researcherid.com/rid/F-4912-2010 -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of Philippe [guest] Sent: Thursday, August 09, 2012 06:07 To: bioconductor at r-project.org; philipp.thomas at vol.at Subject: [BioC] Openening qPCR file from ABI Hi, a colleague of mine gave me a 'sds' file, containing Real-Time PCR data from an ABI machine. I am currently trying to open it using the "ReadqPCR" package, but I am getting errors using it. So maybe someone knows another package/way which I could go to open this file? Best, Philippe -- output of sessionInfo(): R version 2.15.0 (2012-03-30) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ReadqPCR_1.2.0 affy_1.34.0 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affyio_1.24.0 BiocInstaller_1.4.7 preprocessCore_1.18.0 [4] zlibbioc_1.2.0 -- Sent via the guest posting facility at bioconductor.org. _______________________________________________ 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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Hi Philippe, Guido This is indeed the case. E.g. library(HTqPCR) raw.data <- readCtData(files=..., format="SDS") That will give you an object of class qPCRset. From then on you can directly continue using HTqPCR for normalisation, visualisation and testing. Or, if you already have some other workflow in mind, you can simply extract the Ct values into a plain ol' matrix: raw.mat <- getCt(raw.data) best \Heidi > Hi Philippe, > If i recall correctly the package HTqPCR should be able to open ABI's SDS > files. > See chapter 13.1, page 43 of the manual. > http://www.bioconductor.org/packages/2.10/bioc/html/HTqPCR.html > > HTH, > 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://scholar.google.com/citations?user=qFHaMnoAAAAJ > http://www.researcherid.com/rid/F-4912-2010 > > > -----Original Message----- > From: bioconductor-bounces at r-project.org > [mailto:bioconductor-bounces at r-project.org] On Behalf Of Philippe [guest] > Sent: Thursday, August 09, 2012 06:07 > To: bioconductor at r-project.org; philipp.thomas at vol.at > Subject: [BioC] Openening qPCR file from ABI > > > Hi, > > a colleague of mine gave me a 'sds' file, containing Real-Time PCR data > from an ABI machine. I am currently trying to open it using the "ReadqPCR" > package, but I am getting errors using it. So maybe someone knows another > package/way which I could go to open this file? > > Best, > Philippe > > -- output of sessionInfo(): > > R version 2.15.0 (2012-03-30) > Platform: i686-pc-linux-gnu (32-bit) > > locale: > [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C > [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 > [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ReadqPCR_1.2.0 affy_1.34.0 Biobase_2.16.0 > BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] affyio_1.24.0 BiocInstaller_1.4.7 preprocessCore_1.18.0 > [4] zlibbioc_1.2.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 > > _______________________________________________ > 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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