[BioC] HTqPCR only works for 384 qPCR plates
Heidi Dvinge
heidi at ebi.ac.uk
Wed Apr 21 21:50:31 CEST 2010
Hello Andreia,
as Alex mentioned, this is because readCtData expects certain kind of data
to be in specific columns. In your case these are different from the
default columns, which are from exporting data as text files only from the
SDS scanning system.
If changing the columns numbers in readCtData doesn't work, then please
get back to us. Please also note that the readCtData function has extended
functionalities in the current HTqPCR version 1.1.4 compared to the
release version 1.0.0. (basically as I got more different input files to
test), and the latest version of the vignette also contains a longer
description about how to input data into HTqPCR.
HTH
\Heidi
>
> Dear Andreia,
>
> again, have a look at the help page. It will tell you that
> readCtData() has certain expectations about the number
> of certain columns, ie.
>
> flag = 4, feature = 6, type = 7, position = 3, Ct = 8
>
> If your files have that information in a different column,
> you'll have to specify the column number, if they do not
> have it at all you'll have to set it to NULL, as explained
> in the Details section.
>
> In your case the function was looking for columns number
> 3, 4, 6, 7 and 8 in a file with only two or three columns
> which explains the error message.
>
> Cheers,
>
> - axel
>
>
> Axel Klenk
> Research Informatician
> Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil /
> Switzerland
>
>
>
>
> Andreia Fonseca
> <andreia.fonseca@
> gmail.com> To
> axel.klenk at actelion.com
> 04/21/2010 07:06 cc
> PM bioconductor
> <bioconductor at stat.math.ethz.ch>,
> bioconductor-bounces at stat.math.ethz
> .ch
> Subject
> Re: [BioC] HTqPCR only works for
> 384 qPCR plates
>
>
>
>
>
>
>
>
>
>
> Dear Axel,
>
> I have tried and now I have another error i think is due to my
> files:€€ raw<-readCtData(files=files$File, path=path, n.features=80)
> Error in `[.data.frame`(sample, , Ct) : undefined columns selected
>
>
> so in my files I have
>
> gene \t Ctvalue
>
> gene \t Ctvalue \t type(target/endogenous)
>
> should I have a column with the sample number and the condition too?
>
> thanks
> Andreia
>
> On Wed, Apr 21, 2010 at 5:54 PM, <axel.klenk at actelion.com> wrote:
>
> Dear Andreia,
>
> not exactly, it only expects 384 plates...
>
> Try
>
> ?readCtData
>
> and consequently:
>
> raw<-readCtData(files=files$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 at stat.math.ethz.ch>€
> ces at 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 at fm.ul.pt
> andreia.fonseca at gmail.com
>
> [[alternative HTML version deleted]]
>
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> --
> --------------------------------------------
> Andreia J. Amaral
> Unidade de Imunologia Clínica
> Instituto de Medicina Molecular
> Universidade de Lisboa
> email: andreiaamaral at fm.ul.pt
> andreia.fonseca at gmail.com
>
>
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