[BioC] com.braju.sma

[Gordon Smyth]

Dear David,

com.braju.sma is Henrik Bengtsson's very interesting package. Although some 
of us work with Henrik on microarray problems, the com.braju.sma package is 
not associated with bioconductor and isn't designed to work with 
bioconductor functions. You need to send any questions you have to Henrik 
rather than to us!

Best wishes
Gordon

At 03:07 AM 25/06/2003, kfbargad at lg.ehu.es wrote:
>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