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Tutorial 2.2. Expression profiles correlations
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Compare the expression profile of samples using correlations




Files needed:
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We will need the same files as in the tutorial 2.1:

- `gse19188\_median-centered.cdm.gz <http://www.gitools.org/tutorials/data/gse19188_median-centered.cdm.gz>`__ : which contains median-centered log-intensity values divided by standard deviation for 156 samples. 

- `gse19188\_sample\_annotations.txt <http://www.gitools.org/tutorials/data/gse19188_sample_annotations.txt>`__ : which contains the clinical annotation of samples



Perform correlation analysis
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- See  `this chapter <UserGuide_Correlations.rst>`__  for details on how to perform correlation analysis

- Select gse19188\_median-centered.cdm.gz as data file

- Do not select any filtering option

- Apply correlation to columns (as we want to correlate samples)

- Give a name to the analysis. Select a directory where to safe it and click Finish.



Color the columns and rows according to the histology label of the samples and order them
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- In the analysis details tab, click on “heatmap” under “Results” to view the heatmap of the results.

- In properties/columns, select the file “gse19188\_sample\_annotations.txt” and choose “histology” as label to show the type of tumour instead of the id of the sample as column name in the heatmap.

- Select annotate with color to show a color label for the type of histology of the samples.

- Do the same for rows.

- Order the samples by histology by selecting Data>Sort>Sort by label and select columns.

- Change the width and height of the cells in properties/cells to be able to see all the samples in the window and uncheck the options to show the columns and row grid.



Explore the results
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.. image:: img/tutorial-gitoolscasestudy2.2.png

