[BioC] Seeking help to remove control spots in single channel normalization

[Leon Yee]

Hi, Prashantha


Prashantha Hebbar wrote:
> Dear Lee,
> 
> I am thankful to your response. Yes, as you said control information will be
> there in ControlTypes column of featured extract data. But the problem is
> when I give following command for background correction
> 
> Ggene<-backgroundCorrect(RG$G,method='normexp')    #I referred this command
> in mail list
> 
> Ggene variable will not have RG$genes information (i.e. gene list info). If

Since the input of backgroundCorrect is RG$G, which don't contain 
RG$genes information, the result Ggene will surely not contain it. But 
you can still filter the control spot:

Ggene[RG$genes$ControlType==0,]


> I get RG$genes information in next steps (after inter array normalization)
> then only it is possible to remove control spots. 
> 
> So, now my question is If I use directly RG in my background correction (for
> example: Ggene<-backgroundCorrect(RG,method='normexp')), will it create any
> problem? In this case, RG$G-RG$Gb and RG$R-RG$Rb will be done right? So,
> analysis is meaningful right?

I am not know anything about single channel array analysis. But if it is 
two-color array, backgroundCorrect(RG, method=whatever) is OK.

Leon