[BioC] Construction an instance of class marrayRaw

Hinnerk Boriss boriss@izbi.uni-leipzig.de
Sun, 23 Feb 2003 23:34:18 +0100


I am trying to construct an object of class marrayRaw from scratch. I
have red and green intensities stored in data frames that look something
like this:

G_name chip1 chip2 ... chipN
Gene1  0.1   2.	      3.
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),

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


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.