[BioC] PM-intensity and probeset, matrix

[Adaikalavan Ramasamy]

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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