Clustering Matrices Suppose I have a set of 100 $n \times 2$ matrices that all have the following format:
Bid    Profit
[5.00   7.10]
[3.14   6.04]
[2.9    10.08]

Where the numbers are sample values. Now I want to cluster these matrices together using R or some statistical software. How can I do this? I've looked into hclust and time series clustering in R but I don't think this is what I want. 
Edit
In the attached picture, I have three sample matrices plotted. For simplicity's sake I have plotted them all with the same x-values but this may not necessarily be the case. I want a way of saying "at points 3,8,9 (the three highest points on the black curve), this black curve is similar to the blue curve but not the red curve". Ordering of the rows of the matrix should not matter - I can just sort by the first column to ensure that the x-values (Bid) are ordered least to greatest.
edit 2
These graphs are included as if the first column in all three matrices was the same i.e., all three matrices had the form 
xval yval
[a x1]
[b x2]
[c x3]
[d x4]
...

and then the matrices are plotted with the first column on the x-axis and the second column on the y-axis. 
 A: If you needed to cluster whole matrices you would need a special distance measure for matrices.  Fortunately, your situation appears to be much simpler than that.  Given that you are only interested in the third, eighth, and ninth points / rows in each matrix, I would start by throwing all other rows away.  Next, given that these three points will always have identical xval values, you can throw the xval column away (assuming the rows are always in the same order).  You now have 100 vectors of length 3.  
Those can be formed into a new, single matrix by transposing them (into row vectors) and stacking them together.  That is, the first row in the new matrix will be the yvals from the first of the original set of matrices, the second in row two, etc.  In the first column, all the way down, will be the numbers that had corresponded to the third point, the second column the eighth, and the last column the ninth.  Now you have a single matrix with patters to be clustered in rows and the dimensions / feature space within which they will be clustered in the columns.  This is just like any ordinary cluster analysis.  
At this point, you could use whatever distance measure you feel comfortable with and which you think is appropriate for your application (e.g., Euclidean distance).  And you can use whatever clustering algorithm you like and find appropriate (e.g., k-means) likewise.  
