[BioC] PM-intensity and probeset, matrix

[Mohammad Esad-Djou]

Thank you. The solution (b) helped me. 
Best regards,
Mohammad


ramasamy at cancer.org.uk schrieb am 11.06.05 18:51:18:
> 
> Sorry did not see your second question. There are two of doing this
> 
> a) Use the sapply version of the solution below to get a matrix followed
> by matplot(con, pms) but you will have to redefine 'con' slightly.
> 
> b) Use the lapply version with matpoints. Example :
>   
>    pm.values <- lapply( ps, pm )
>    matplot( con, pm.values[[1]], type="n", ylim=c(30,20000) )
>    for( i in 1:length(pm.values) ){ matpoints( con, pm.values[[i]] ) }
> 
> 
> I think you might prefer the second solution.
> 
> 
> 
> On Sat, 2005-06-11 at 17:34 +0100, Adaikalavan Ramasamy wrote:
> > Yes. Here is an example :
> > 
> >  raw <- ReadAffy()
> >  ps  <- probeset(raw, 
> >                  genenames=c("203508_at","204563_at", "204513_s_at"))
> > 
> > Now you can use either lapply or sapply.
> > 
> >  pms1 <- lapply( ps, pm )
> >  pms2 <- sapply( ps, pm )
> > 
> > Now 'pms1' will be a list while 'pms2' would be a matrix.
> > 
> > Regards, Adai
> > 
> > 
> > 
> > On Fri, 2005-06-10 at 21:13 +0200, Mohammad Esad-Djou wrote:
> > > Hello all,
> > > 
> > > I would like to extract PM value of 3 probeset and the result with matplot represent.
> > > I wrote this small program:
> > > 
> > > ps<- probeset(data.raw, genenames = c("203508_at","204563_at", "204513_s_at"))
> > > 
> > > pms1<- pm(ps[[1]])
> > > pms2<- pm(ps[[2]])
> > > pms3<- pm(ps[[3]])
> > > 
> > > con <- matrix(c(0, 0.125,0.25,0.5,1,2,4,8,16,32,64,128,256,512), 11, 42, byrow = TRUE)
> > > 
> > > matplot(con, pms1, log = "xy", main = "PM", ylim = c(30, 20000))
> > > points(con, pms2)
> > > points(con, pms3)
> > > 
> > > 
> > > I get the expected result but I have 2 questions:
> > > 
> > > 1. Can I all value of PM extract at one time? If yes, how?
> > > pms.all <-  pm(ps????)
> > > 
> > > 2. If answer of the first question is negative, can I 3 matrix combine? 
> > > Because I use in my main program several probeset, I do not want to use POINTS.
> > > I would like only matplot use. 
> > > 
> > > Thanks,
> > > Mohammad Esad-Djou
> > > 
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> 


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