[BioC] limma neqc

[Ina Hoeschele]

Hi Gordon et al.,
   I am confused about something - I am using limma neqc and according to a recent paper (Shi, Oshlack, Smyth 2010) the quantile normalization should be performed using both positive and negative control probes. But in the arguments for neqc one can specify the identifier for negative control probes and "regular" probes. So I set negctrl="negative" and regular="Gene". But this does not allow me to specify positive control probes?
Many thanks, Ina