MATLAB: Forming a cell array from matrix

datamining

I want to include the genes included in each cluster .

i have genedata =[1:1:100]

the code given below is for number of genes in cluster. Now i want to include the genes included

genedata=[1:1:100]
IDX = kmeans(genedata',20)
for i = 1:20
  genenum(i) = sum(IDX == i);
end

http://www.mathworks.in/matlabcentral/answers/21485-clustering-the-data

Best Answer

First off, the loop you have is okay, but you could also replace it with the more efficient

genenum = accumarray(IDX(:));

As for including the genes included: you are not clear as to what you mean by that, so I will guess:

genes = cell(20,1);
for K = 1 : 20
  genes{K} = genedata(IDX==K);
end

Related Solutions

MATLAB: Error CAT arguments dimensions are not consistent.

genedata=1:100;
IDX = kmeans(genedata',20);
genenum = cell(20,1);
for i = 1:20
    genenum{i} = sum(IDX == i);
end
genes = cell(20,1);
for K = 1 : 20
    genes{K} = genedata(IDX==K);
end
final=[num2cell((1:20)') genenum genes];

variant 2

genedata=1:100;
IDX = kmeans(genedata,20);
genenum = histc(IDX,1:20);
genes = [(1:20)', genenum, zeros(20,max(genenum))];
for i1 = 1:20
    c = genedata(IDX==i1);
    genes(i1,3 + (0:numel(c)-1)) = c;
end

MATLAB: Clustering the data

OK, so from what I understand, you are clustering the genes, and not the samples, which means that you need to transpose your sample-gene matrix, and then run kmeans. If you then type in:

IDX = kmeans(genedata',20); %where genedata is a matrix containing genes in rows, and samples in columns,

IDX will contain 100 elements, which contains numbers from 1 to 20, corresponding to which cluster the gene is in.

for i = 1:20
genenum(i) = sum(IDX == i);
end

and genenum will contain the number of genes in each cluster. You could alternatively take the histogram of IDX, and the resulting array will contain the same info as genenum.

If you'd want to include the genes included in each cluster as well, you can't store it in the same matrix as the numbers of elements are not the same in each 'cell' of the matrix, and hence I advise using cell variables instead. Hope this answers your questions!

Best Answer

Related Solutions

MATLAB: Error CAT arguments dimensions are not consistent.

MATLAB: Clustering the data

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