Hi Wolfgang, I have 4 different positive controls in my screen and I want to use ?NPI? method to normalize the plates. Whether can I define the specific one as the positive control to be applied to this method? The following is the partial scripts about positive controls posControls <- vector("character", length=dim(Data(x))[3]) posControls[1] <- list(act="(?i)^ntc2pluslps$", inh="(?i)^myd88$|^tlr4$|^irak1and4$") posControls[2] <- list(act="(?i)^ntc2pluslps$", inh="(?i)^myd88$|^tlr4$|^irak1and4$") So how can I use ?ntc2pluslps? in channel 1 as the specific positive control? Many thanks Ning

Dear Ning in a post like this, please remember next time to state the package and the function name that you are refering to. This will help people reading this list (which covers a wide range of packages and concepts) better realise what you are talking about. Also, please tell us what you have already tried, where/why this failed, a code example that can be reproduced by others, and please report precisely the error message or unsatisfactory behaviour that you get. Such basic courtesy makes it much easier to give a useful reply. So, the topic is the "normalizePlates" function in the "cellHTS2" package. It is always good to look at the manual page of a function that you want to use. In your case, the manual page of "normalizePlates" says Arguments: posControls: a vector of regular expressions giving the name of the positive control(s). See details. The code fragment below confuses list and vector syntax. It results in posControls being > posControls [[1]] [1] "(?i)^ntc2pluslps$" [[2]] [1] "(?i)^ntc2pluslps$" which is likely not what you intended. OTOH, have you tried with posControls = rep("(?i)^ntc2pluslps$", 2) This would set only wells matching that regular expression as the positive controls for both color channels. Best wishes Wolfgang Il Nov/2/10 2:19 PM, Ning ha scritto: > Hi Wolfgang, > > I have 4 different positive controls in my screen and I want to use ?NPI? method > to normalize the plates. > Whether can I define the specific one as the positive control to be applied to > this method? > > The following is the partial scripts about positive controls > > posControls<- vector("character", length=dim(Data(x))[3]) > posControls[1]<- list(act="(?i)^ntc2pluslps$", > inh="(?i)^myd88$|^tlr4$|^irak1and4$") > posControls[2]<- list(act="(?i)^ntc2pluslps$", > inh="(?i)^myd88$|^tlr4$|^irak1and4$") > > So how can I use ?ntc2pluslps? in channel 1 as the specific positive control? > > > Many thanks > Ning > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor