[BioC] Construction an instance of class marrayRaw

[Jean Yee Hwa Yang]

Hi Hinnerk,

It is likely that matrix(red) isn't a M by N matrix.  Check 
dim(matrix(red))
class(matrix(red))

In addition, try the following:
exp2raw <- new("marrayRaw", maRf=as.matrix(red), maGf=as.matrix(green))
exp2raw

To get a matrix of log-ratios, use
maM(exp2raw)

Hope this helps

Jean

> GeneM 2.     4.          5.
> 
> Then I tried the following:
> 
> > infos <- new("marrayInfo", maLabels=dimnames(green)[[1]])
> > exp2raw <- new("marrayRaw", maRf=matrix(red), maGf=matrix(green),
> maTargets=infos)
> 
> Now looking at the object reveals that something went wrong: (btw: I was
> having 10 chips)
> 
> > exp2raw
> Pre-normalization intensity data:	 Object of class marrayRaw. 
> 
> Number of arrays: 	1 arrays.
>  
> A) Layout of spots on the array: 
> Array layout:	 Object of class marrayLayout. 
> 
> Total number of spots:			
> Dimensions of grid matrix:		 rows by  cols
> Dimensions of spot matrices:		 rows by  cols
> 
> Currently working with a subset of  spots.
> 
> Control spots: 
> 
> 
> Notes on layout: 
> 
> 
> B) Samples hybridized to the array: 
> Object of class marrayInfo. 
> 
>  [1] "A" "B" "C" "D" "E" "F" "G" "H" "I" "K"
>  ...
> 
> Number of labels:  348  
> Dimensions of maInfo matrix:   rows by   columns
> 
> Notes: 
> 
> 
> C) Summary statistics for log-ratio distribution: 
>      Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 
> [1,]   NA      NA     NA   NA      NA   NA   10
> 
> D) Notes on intensity data: 
> 
> ----------
> What am I missing here. There is apparently only one chip recognized,
> even though I supplied a matrix with 10 columns. Do I need to specify a
> layout? Right now I don't really care about spacial effects, that's why
> I didn't bother playing with it. I hope you can help me to bring me on
> the right track.
> 
> Cheers,
> Hinnerk
> 
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