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 Cl?nica
> 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 Cl?nica
> Instituto de Medicina Molecular
> Universidade de Lisboa
> email: andreiaamaral at fm.ul.pt
> ? ? ? ? ?andreia.fonseca at gmail.com
>
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