[BioC] HTqPCR only works for 384 qPCR plates

Wed Apr 21 19:44:31 CEST 2010

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>,
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                                       .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

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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

The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged.
It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email.
The content of this email is not legally binding unless confirmed by letter.
Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com 