[BioC] concentrations

[Mohammad Esad-Djou]

Hallo all,
thank you very much for your suggestions.

> Next time, please learn to ask the question more clearly (with example
> of the desired output) to avoid the rest of guessing (e.g. what do you
> mean by "correctly finding numeric values").

Yes.  You are right. I try to reformulate my question. I would like to compute concentrations for different ProbeSet. 
I used SpikeIn example in 

Description of affy
Laurent Gautier, Rafael Irizarry, Leslie Cope, and Ben Bolstad
April 21, 2005

page 22:

> data(SpikeIn)
> pms <- pm(SpikeIn)
> mms <- mm(SpikeIn)
> par(mfrow = c(1, 2))
> concentrations <- matrix(as.numeric(sampleNames(SpikeIn)), 20,
+ 12, byrow = TRUE)
> matplot(concentrations, pms, log = "xy", main = "PM", ylim = c(30,
+ 20000))
> lines(concentrations[1, ], apply(pms, 2, mean), lwd = 3)
> matplot(concentrations, mms, log = "xy", main = "MM", ylim = c(30,
+ 20000))
> lines(concentrations[1, ], apply(mms, 2, mean), lwd = 3)


I wrote:
>library(affy)
>data.raw <- ReadAffy(filenames="./R/ME_cel/Expt1_R1.CEL", ....)
>pset1 <- probeset(data.raw,geneNames(data.raw)[1])

Test:
>pset1
$"1007_s_at"
ProbeSet object:
  id=1007_s_at
  pm= 16 probes x  4  chips

and:
> SpikeIn
ProbeSet object:
  id=AFFX-BioB-5_at
  pm= 20 probes x  12  chips

R program calls both objects ProbeSet, but I cannot go same way as above example: (e.g.)

> pms <- pm(pset1)
Error in pm(pset1) : No direct or inherited method for function "pm" for this call

> sampleNames(pset1)
Error in sampleNames(pset1) : No direct or inherited method for function "sampleNames" for this call

> sampleNames(SpikeIn)
 [1] "0.50"   "0.75"   "1.00"   "1.50"   "2.00"   "3.00"   "5.00"   "12.50" 
 [9] "25.00"  "50.00"  "75.00"  "150.00"


My main question:
1. How can I compute concentrations for different ProbeSet?

2. What didn't I consider for ProbeSet (SpikeIn and pset1)?

Thanks,
Mohammad Esad-Djou