[BioC] PM-intensity and probeset, matrix

[fhong@salk.edu]

>
> 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????)
library(affy)
pm(affybatch.object  ## in your case data.raw

Fangxin

> 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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--------------------
Fangxin Hong  Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu
(Phone): 858-453-4100 ext 1105