Data Import and Processing

You can find the NetWalker workspace files generated in this tutorial in the Downloads.

  1. Start NetWalker and select NIK 1 as knowledgebase. Wait till the Knowledgebase is loaded.
  2. Click “Import Dataset” button  on the toolbar, select “Tab-delimited text files” in the File filter, and load dataset “Samples/Doxorubicin_MCF7.txt” found in your NetWalker installation folder, or you can also download it from this web site from the Downloads. The dataset will be opened in a TableView window. Here, there are several functions for data processing, such as log-transforming, reverse-transforming from log, averaging, standard deviations, etc…
  3. Normalize the data by the average of rows:
         a.  Select all data columns (i.e. those except the Names column) and take average . A new column containing averages of data across each row will appear.
         b.  Select the newly generated column for averages and set as control ( button).
         c.  Select the data columns you selected in (a) again and take ratio click  (ratio) to divide values in each row in each sample by the average of value across all values in the row.
         d.  Select the newly generated row-normalized 8 columns and take log2 ( then OK) to have log2-transformed row-normalized data. You should have 26 total columns now: 1 column of gene names, 8 columns of original data, 1 column of averaged rows, 8 columns of ratio values and 8 columns of log2 transformed ratio values. You can remove the 8 columns of original raw untransformed data now. Retain the ratio columns as these will be used later for NetWalk analyses.

    This is what you should see after removing the original untransformed data (select the 8 original data columns and hit  ).

    As you can imagine, most procedures for row-based normalizations or processing can be performed by sequential utilization of the mathematical operations in the TableView toolbar. We will leave deriving the procedure for z-score normalization of data rows to you as an exercise. Z-score normalization is done by

    where xij is the data value at row i and column j, µi is the mean and σi is the standard deviation of the whole row i.

  4. In NetWalker, data can be freely exchanged between external applications. In order to transfer the generated dataset to Excel, select the desired columns or rows, press “Ctrl + C”, go to Excel, and paste with “Ctrl + V”.
  5. Similarly, datasets can be imported into NetWalker from external spreadsheet applications (e.g. Excel). Copy the data that you just pasted into Excel, then in NetWalker, go to View menu and select Paste. Select “Create a TableView” and press OK. The next message will ask if you want to treat the first row as column header names, say no. A new TableView window will be created containing the copied cells from the spreadsheet.