[BioC] duplicateCorrelation

[Gordon Smyth]

At 10:25 PM 13/06/2004, Jason Skelton wrote:
>Hi
>
>I'm having difficulty with a design matrix in the duplicateCorrelation 
>function in limma
>I have 15 slides and M values for each of them: [,1] to [,15]
>however when I specify the following matrix
>
>   W2minusW0 M2minusM0 M2minusW2 M0minusW0 M22minusM20 M22minusW2 M20minusW0
>1          0         0         0         0           0          0         -1
>2          0         0         0         0           0          0          1
>3          0         0         0         0           0          1          0
>4          0         0         0         0           0         -1          0
>5          0         0        -1         0           0          0          0
>6          0         0         1         0           0          0          0
>7          0         0         0         0           1          0          0
>8          0         0         0         0          -1          0          0
>9          0         0         0        -1           0          0          0
>10         0         0         0         1           0          0          0
>11         1         0         0         0           0          0          0
>12        -1         0         0         0           0          0          0
>13         0         1         0         0           0          0          0
>14         0        -1         0         0           0          0          0
>15        -1         0         0         1           0          0          0
>
>cor <- duplicateCorrelation(object$M, design="designmatrix",spacing=648)

The design matrix must be a _matrix_. You've input a character string. This 
would not work in any version of limma.

If "designmatrix" is the name of your matrix, perhaps you simply need to 
remove the double-quotes.

Gordon

>Error in duplicateCorrelation(object$M, design = "designmatrix",  :
>        Number of rows of design matrix does not match number of arrays
>
>I only appear to have had this problem since I changed limma versions ???
>
>using R 1.9.0
>limma 1.6.7
>
>Does anyone know of a easy way either contruct the above matrix
>OR
>check wether the matrix is suitable for dupcor....
>
>I've tried both matrix and dataframes both with the same error
>
>any help greatly recieved
>Jason