Interpreting COXEN Results

When calculations for your uploaded files complete, you will be directed to the datasets page, where you will find new results files in the corresponding dataset.

New files

If all goes according to plan you will have two or more results files:

  1. A prediction file
  2. A quality control file
  3. You may observe different files depending on whether the .CEL files you uploaded were of the incorrect type or accidentally corrupted or truncated.

QUALITY CONTROL

The quality control file includes an assessment of the uploaded files. For each file analyzed, this file lists:

  1. The Filename
  2. Whether the file was able to be read completely
  3. The type of chip
  4. The average correlation coefficient of expression
  5. Whether the correlation coefficients are sufficently high as to allow the prediction values to be considered trustworthy.

PREDICTIONS

With the exception of the first and last columns, each column in the prediction file corresponds to one particular CEL file, as listed in the third row. The first two rows illustrate whether the expression values in the CEL file correlate with our datasets enough that the prediction results are credible. If a CEL file fails the correlation criterion (by having a low mean correlation coefficient) this may mean that there was a problem with the analysis of the genechip.

Below the first rows are listed, from left to right, compounds for which COXEN tested, the prediction scores for the various compounds and CEL files, and finally, whether the program was successfully able to calculate prediction scores for that compound.