[BioC] Construction an instance of class marrayRaw
Jean Yee Hwa Yang
Sun, 23 Feb 2003 15:15:16 -0800 (PST)
It is likely that matrix(red) isn't a M by N matrix. Check
In addition, try the following:
exp2raw <- new("marrayRaw", maRf=as.matrix(red), maGf=as.matrix(green))
To get a matrix of log-ratios, use
Hope this helps
> GeneM 2. 4. 5.
> Then I tried the following:
> > infos <- new("marrayInfo", maLabels=dimnames(green)[])
> > exp2raw <- new("marrayRaw", maRf=matrix(red), maGf=matrix(green),
> 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.
>  "A" "B" "C" "D" "E" "F" "G" "H" "I" "K"
> Number of labels: 348
> Dimensions of maInfo matrix: rows by columns
> 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.
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