Dear Axel,

I have tried and now I have another error i think is due to my files:

 raw<-readCtData(files=files$File, path=path, n.features=80)
Error in `[.data.frame`(sample, , Ct) : undefined columns selected


so in my files I have

gene \t Ctvalue

gene \t Ctvalue \t type(target/endogenous)

should I have a column with the sample number and the condition too?

thanks
Andreia

On Wed, Apr 21, 2010 at 5:54 PM, <axel.klenk@actelion.com> wrote:

>
> Dear Andreia,
>
> not exactly, it only expects 384 plates...
>
> Try
>
> ?readCtData
>
> and consequently:
>
> raw<-readCtData(files=files$File, path=path, n.features=80)
>
> Cheers,
>
>  - axel
>
>
> Axel Klenk
> Research Informatician
> Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
> Switzerland
>
>
>
>
>             Andreia Fonseca
>             <andreia.fonseca@
>             gmail.com>                                                 To
>             Sent by:                  bioconductor
>             bioconductor-boun         <bioconductor@stat.math.ethz.ch>
>             ces@stat.math.eth                                          cc
>             z.ch
>                                                                   Subject
>                                       [BioC] HTqPCR only works for 384
>             04/21/2010 06:29          qPCR plates
>             PM
>
>
>
>
>
>
>
>
>
> Dear all,
>
> I have data for 80 miRNAs produced with qPCR plates, I am trying to use
> HTqPCR but I am receiving an error, due to this. bellow is the error
> message
> and the session info.
> thanks
> regards,
> Andreia
>
> > raw<-readCtData(files=files$File, path=path)
> Error in readCtData(files = files$File, path = path) :
>  384 gene names (rows) expected, got 80
>
>
>
>
> > sessionInfo()
> R version 2.10.1 (2009-12-14)
> x86_64-pc-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] qpcrNorm_1.4.0     affy_1.24.2        HTqPCR_1.0.0
> limma_3.2.1
> [5] RColorBrewer_1.0-2 Biobase_2.6.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.14.0        gdata_2.7.1          gplots_2.7.4
> [4] gtools_2.6.1         preprocessCore_1.8.0 tools_2.10.1
> --
> --------------------------------------------
> Andreia J. Amaral
> Unidade de Imunologia Clínica
> Instituto de Medicina Molecular
> Universidade de Lisboa
> email: andreiaamaral@fm.ul.pt
>         andreia.fonseca@gmail.com
>
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-- 
--------------------------------------------
Andreia J. Amaral
Unidade de Imunologia Clínica
Instituto de Medicina Molecular
Universidade de Lisboa
email: andreiaamaral@fm.ul.pt
         andreia.fonseca@gmail.com

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