[BioC] cellHTS: help for NPI normalization

Klaus-Peter Pleissner pleissner at mpiib-berlin.mpg.de
Fri May 9 10:24:26 CEST 2008

Dear all,

using cellHTS (not cellHTS2) we want to perform a "NPI-normalization" 
with positive and negative control wells.

According twoway. pdf vignette we define  control wells  as :

posCtr <- list(act= "(?i)^Mock$", inh = "(?i)^NP$")
negCtr <- "(?i)^Allstars$"

and normalize by

x <- normalizePlates(x, normalizationMethod="NPI",negControls=negCtr, 

We get an error:

Error in NPI(x, posControls, negControls) :
  'posControls' should be a vector of regular expressions with length 1

Enter a frame number, or 0 to exit  

1: normalizePlates(x, normalizationMethod = "NPI", negControls = negCtr, 
2: switch(normalizationMethod, mean = scaleByPlateMean(x), median = 
3: NPI(x, posControls, negControls)

If we are using  a negative normalization  method ( as descibed in the 
x <- 

this error doesn't occur.

What is wrong in the definition of positive control wells ?
Thanks is advance for help.


Mit freundlichen Grüssen / Best regards

Dr. Klaus-Peter Pleissner
Max Planck Institute for Infection Biology
Core Facility Bioinformatics
Charitéplatz 1
D-10117 Berlin

*Phone:* +49-30-28460-119
*Fax:*   +49-30-28460-507
*URL:*   http://web.mpiib-berlin.mpg.de/bioinformatik <http://web.mpiib-berlin.mpg.de/bioinformatik/>
*Email:* pleissner at mpiib-berlin.mpg.de  <mailto:pleissner at mpiib-berlin.mpg.de>

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