[BioC] <no subject>

[Mohammad Esad-Djou]

Hello all,

I would like to use spikein and HGU-133ATAG experiment for Concentrations comparison.  
The relationship between Spikein and HGU-133ATAG is still unclear to me.  
I have a small program, which runs with SpikeIn in affy Package without errors:

data(SpikeIn)
pms <- pm(SpikeIn)
mms <- mm(SpikeIn)
concentrations <- matrix(as.numeric(sampleNames(SpikeIn)), 20, 12, byrow = TRUE)

par(mfrow = c(1, 2))
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)

Now I would like to run same test with Hg-U133ATAG. 
My algorithm has 5 steps:  
A.  READ *.CEL file --> data.raw (AffyBatch Object) 
B. extract probe sets from AffyBatch Object --> pset 
C. INIT.  PM and MM from pset 
D. Calculate Concentrations (if NA THEN pset = pset[!is.na(pset) ]) 
E. matplot for PM and MM

afterwards I write in R:

# Upto 42 Experiments: 
library(affy)
data.raw <- ReadAffy(filenames="H:/Profile/Eigene Dateien/Dip_bak/Pr_sprach/R/ME_cel/Expt1_R1.CEL")
ps <- probeset(data.raw)
pms <- pm(ps[[1]])
mms <- mm(ps[[1]])

#concentrations <- matrix(as.numeric(sampleNames(ps[[1]])), 20, 1, byrow = TRUE)
#Warning message: 
#NAs introduced by coercion 

psna = ps[[1]][!is.na(ps[[1]])]
concentrations <- matrix(as.numeric(sampleNames(ps[[1]])), 16, 1, byrow = TRUE)

# No Answer!?

I cannot find my source of error. Can Someone help me?

Thanks,
Mohammad Esad-Djou