[BioC] affy: How to back transform the matrix to a vector? (low-level imaging)

[Kasper Daniel Hansen]

On Jan 31, 2006, at 4:34 PM, Simon Lin wrote:

> I am trying to transform the vector (pm and mm) extracted from  
> @exprs to a
> matrix (2-D layout), so an image can be plotted. It works out.

Yes. I assume the code given below has been snapped from
   getMethod("image", "AffyBatch")\

(Why do you want to generate that code anyway, when suitable image  
functions exists?)


>
>
> Now, when I back-transform the image matrix to the vector, there  
> are some
> trouble. See the code below.
>
>
>
> Seems that the matrix has to be transposed somehow. Any ideas?
> Thanks! -Simon
>
>
>
>    library (affy)
>
>    data (affybatch.example) # has 3 chips
>
>    x<- affybatch.example
>
>    m.vector <- log2( x at exprs[, 2]) # take the second array
>
>
>
>    x.pos <- (1:nrow(x)) - (1 + getOption("BioC")$affy$xy.offset)
>
>    y.pos <- (1:ncol(x)) - (1 + getOption("BioC")$affy$xy.offset)
>
>    # from vector to matrix
>
>    m <- as.matrix(rev(as.data.frame(matrix(m.vector, nrow = length 
> (x.pos),
>
>                 ncol = length(y.pos)))))

If you debug this line, you will understand why a simple as.matrix  
does not work. Basically, first a matrix is created. It is then  
converted to a data.frame so that rev() works on columns. Look:

 > matrix(1:9, nrow = 3)
      [,1] [,2] [,3]
[1,]    1    4    7
[2,]    2    5    8
[3,]    3    6    9
 > as.data.frame(matrix(1:9, nrow = 3))
   V1 V2 V3
1  1  4  7
2  2  5  8
3  3  6  9
 > rev(as.data.frame(matrix(1:9, nrow = 3)))
   V3 V2 V1
1  7  4  1
2  8  5  2
3  9  6  3
 > as.matrix(rev(as.data.frame(matrix(1:9, nrow = 3))))
   V3 V2 V1
1  7  4  1
2  8  5  2
3  9  6  3
 > as.vector(as.matrix(rev(as.data.frame(matrix(1:9, nrow = 3)))))
[1] 7 8 9 4 5 6 1 2 3

Ok?

/Kasper


>
>
>    # ????????????????
>
>    # from matrix to vector
>
>    m0.vector<- as.vector (m) # this does not work, need some  
> massage of m
>
>    # see if it works
>
>    sum (m.vector!= m0.vector)
>
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