[BioC] PM-intensity and probeset, matrix
ramasamy at cancer.org.uk
Sat Jun 11 18:34:24 CEST 2005
Yes. Here is an example :
raw <- ReadAffy()
ps <- probeset(raw,
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.
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[])
> pms2<- pm(ps[])
> pms3<- pm(ps[])
> 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.
> Mohammad Esad-Djou
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