Problem using quantilenorm() with DataMatrix objects

Hi Everyone,

I am trying to perform quantile normalization on some microarray data (I've imported the data as a DataMatrix object), but I'm getting an error. The following is my code:

%%Import all Bioinformatics Toolbox Functions and Constructors
import bioma.data.*
import bioma.util.*

%%Open Excel with Microarray Data
% Creates a DataMatrix object
DM = DataMatrix('File','IntensityOnly_NN_Ordered.xls');

%%Quantile Normalization
NormDM = quantilenorm(DM);

But I get this error:

??? Undefined function or method 'sort' for input arguments of type 'bioma.data.DataMatrix'.

    Error in ==> quantilenorm at 86
        [sortedVals,ndx(:,col)] = sort(values(:,col));

    Error in ==> NormalizeAndFilter at 17
    NormDM = quantilenorm(DM);

I am using Matlab R2011a with the latest Bioinformatics Toolbox on a Windows 7 64-bit computer.

I would appreciate any thoughts on this.

Many thanks, David

Answer 1

[Paulo Silva]

You can't use the MATLAB sort function on those DataMatrix, at least not directly, see this functions

sortcols %sort the columns of the DataMatrix

sortrows %sort the rows of the DataMatrix

double %convert the DataMatrix to one MATLAB Array and you can use the sort function