Question: TIGRESS error on dataTest
0
gravatar for pengchy
2.6 years ago by
pengchy410
China/Beijing
pengchy410 wrote:

Hi, I have downloaded the TIGRESS package from http://projets.cbio.mines-paristech.fr/~ahaury/svn/dream5/html/index.html, and test the test data with the following matlab code, and got the error message listed as following codes:

cd /path/to/TIGRESS/    
load('data/dataTest.mat')

>>test.net = tigress(dataTest)
Found 20 genes, 10 experiments, 4 transcription factors

L = 5 
alpha = 0.200000 
R = 1000 
Algorithm : lars 

Now working on target 1 out of 20 
??? Improper assignment with rectangular empty matrix.

Error in ==> lars at 94
        [gamma(i) min_i min_j] = minplus(gammaTest);

Error in ==> stability_selection at 53
        path=lars(xs(i1,:), y(i1), 'lar',L);

Error in ==> tigress at 115
        tmp=stability_selection(x,y,ntf,find(predTF),R,L,alpha,LarsAlgo);

But when the L is set to 3, the test will successful:

>> freq=tigress(dataTest,'R',R,'alpha',alpha,'L',L)
Found 20 genes, 10 experiments, 4 transcription factors

L = 3 
alpha = 0.300000 
R = 500 
Algorithm : lars 

Now working on target 1 out of 20 
Elapsed time is 0.558753 seconds.
Now working on target 2 out of 20

When I test on my own data, another error occurred:

>> freq = tigress(lmi_data,'R',R,'alpha',alpha,'L',2)
Found 17119 genes, 129 experiments, 957 transcription factors

L = 2 
alpha = 0.300000 
R = 500 
Algorithm : lars 

Now working on target 1 out of 17119 
??? Index exceeds matrix dimensions.

Error in ==> stability_selection at 55
        freq(:,predictorTF)=freq(:,predictorTF) + abs(sign(path(2:L+1,:)));

Error in ==> tigress at 115
        tmp=stability_selection(x,y,ntf,find(predTF),R,L,alpha,LarsAlgo);

Could anyone help me out? Thank you!

trn tigress grn • 686 views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by pengchy410

I have solved the problem on my own data by:

lmi_data = rmfield(lmi_data,'tf_index')
ADD REPLYlink written 2.6 years ago by pengchy410
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