[BioC] Order in which ReadAffy() and read.affybatch()

[Hrishikesh Deshmukh]

Hello All,

I have questions about the order in which ReadAffy()
and read.affybatch() reads in affy CEL files. I need
this piece of information because i want to label the
arrays when i look at hist() and boxplot(). I want to
make sure that right labels (filenames) are displayed
for its corresponding lines/boxplots. 

Is there a book specifically on BioC, this would be a
big help?

In general on what basis does one accept/reject arrays
from a pool of replicates! The hist() and boxplot()
shows clearly that all the arrays (replicates) do not
show the same "behaviour".

Here are the code fragments:
library(affy)
library(hgu95av2cdf)
library(hgu95av2probe)
library(matchprobes)
data(hgu95av2probe)
summary(hgu95av2probe)
file.names<-c("1.CEL",  "2.CEL",  "3.CEL",  "4.CEL", 
"5.CEL","6.CEL","7.CEL",  "8.CEL",  "9.CEL", 
"10.CEL", 
"11.CEL","12.CEL","13.CEL",14.CEL","15.CEL","16.CEL","17.CEL")
M<-read.affybatch(filenames=file.names,
description=NULL,notes="",compress=F,   
m.mask=F,rm.outliers=F,rm.extra=F,verbose=T)
hist(M)
legend(12,1.2,sampleNames(M),col=1:17,lty=1:17) 

When i run the legend line i see hist() displays
different "lines" and legend does not match correctly!

Thanks in advance.
Hrishi