[BioC] Openening qPCR file from ABI

[Heidi Dvinge]

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.
>
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