[BioC] The question about “NPI” normalization method

[Wolfgang Huber]

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
>
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