# [BioC] Construction an instance of class marrayRaw

**Jean Yee Hwa Yang
**
jean@biostat.ucsf.edu

*Sun, 23 Feb 2003 15:15:16 -0800 (PST)*

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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