[BioC] cellHTS: help for NPI normalization

[Klaus-Peter Pleissner]

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, 
posControls=posCtr,transform=log)



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, 
posCo
2: switch(normalizationMethod, mean = scaleByPlateMean(x), median = 
scaleByPla
3: NPI(x, posControls, negControls)



If we are using  a negative normalization  method ( as descibed in the 
vignette)
x <- 
normalizePlates(x,normalizationMethod="negatives",negControls=negCtr, 
posControls=posCtr,transform=log)

this error doesn't occur.


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

Klaus-Peter
-- 

Mit freundlichen Grüssen / Best regards

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

*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>