[BioC] com.braju.sma

[kfbargad at lg.ehu.es]

Dear all,

sorry to bother again but I have been following the examples from the 
com.braju.sma manual with some of my data and have seen some warnings 
that I would like to understand, if anyone is so kind to explain me.

I am using QuantArray .txt files for two colour chips.

1.- I wanted to extract the signal from the chips without doing 
background subtraction and therefore wrote the following

> ma<-getSignal(raw, bg.subtract=FALSE)
Warning message: 
Argument 'bg.subtract' in getSignal() (class RawData) is deprecated. 
Please use 'bgSubtract' instead. in: getSignal.RawData(raw, 
bg.subtract = FALSE) 

but it still performs the calculation (as you can see below). Should I 
use bgSubtract instead as stated on the message?
> ma
[1] "MAData: M (12288x6), A (12288x6), Layout: Grids: 12x4 (=48), 
spots in grids: 16x16 (=256), total number of spots: 12288. Spot id's 
are specified."

2.- Also, I wanted to have a look at the A values, but instead got the 
following answer
> ma$A
[1] "SpotSlideArray: 2003-06-24 18:01:02"

What should I type?

3.- Finally, I normalised the chips using Lowess and got another 
warning:

> normalizeWithinSlide(ma, method="l")
Warning messages: 
1: Collapsing to unique x values in: approx(line, xout = A[ok]) 
2: Collapsing to unique x values in: approx(line, xout = A[ok]) 
3: Collapsing to unique x values in: approx(line, xout = A[ok]) 
4: Collapsing to unique x values in: approx(line, xout = A[ok]) 
5: Collapsing to unique x values in: approx(line, xout = A[ok]) 
6: Collapsing to unique x values in: approx(line, xout = A[ok]) 

but again the calculation is performed. What does this mean?

Thanks ever so much for your help.

David