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Alicia Amadoz, 05/27/2010 08:42 am


Clustering Input Form

Online examples

Here you can load small datasets from our server. You can use them to run examples and see how the tool works. Click on the links to load the data.

Select your data

Here you can select the dataset you want to cluster. You should have uploaded it previously using the Upload Menu in Babelomics and tagged it with the Data matrix - Expression data type.

Required input data

Input data matrix should be in a plain text file as following:

# some comments
# more comments
#NAMES Cond1 Cond2 Cond3 Cond4 Cond5 Cond6
gen1    -3.06    -2.25    -1.15    -6.64    0.40    1.08
gen2    -1.36    -0.67    -0.17    -0.97    -2.32    -5.06
gen3    -0.17    0.48    1.23    1.52    1.11    
gen4        1.61    -0.27    0.71    -0.62    0.14
gen5    2.09    2.12    2.62    1.95    1.04    2.18
gen6    0.20    -3.06    -0.03    0.64    0.84    
gen7    -2.00    -0.64    -0.29    0.08    -1.00    
gen8    0.93    1.29    -0.23    -0.74    -2.00    -1.25
gen9    0.88    0.31    -0.22    3.25        
gen10    0.71    1.03    -0.25        1.03    

Matrix rows correspond to genes and matrix columns correspond to conditions (arrays).
All the data items must be separated by tabulators.
There is no special character for missing values, simply leave these places empty.
All lines beginning with "#" are treated as commentaries. The first one with #NAMES is mandatory.

See EXPRESSION MATRIX section for more details.

Select type of clustering

Select how you want to cluster input data. You can choose samples and/or genes.

Select method

Select the method you want to use for the analysis.

  • UPGMA
  • SOTA
  • K-means

See METHODS section for details on the algorithms.

Select distance

Select the distance you want to use for the analysis.

  • Euclidean (normal)
  • Euclidean (square)
  • Correlation coefficient (Spearman)
  • Pearson correlation coefficient

See METHODS section for details on the algorithms.

Job

Here you can set a name and a description for the analysis you are running. If you leave name empty your job will be named as untitled by default.

Run

Once all options are set you can run the job. You may get some error message if some parameters are not properly set. If you do, just check the options you have chosen.

See RESULTS section for details on the result data format and plots.