If a Partek Flow task fails (no report is produced), please follow the directions in Reporting a problem.

If the task report is produced, but the results are missing for some features (Figure 1), it may be because something went wrong with the estimation procedure. To better understand this, use the information available in the Extra details report (Figure 1). This type of information is present for many tasks, including Differential Analysis and Survival Analysis.

Figure 1. Use “View extra details report” button to see why the results are missing.

Click the Extra details report icon for the feature of interest (Figure 1). This will display the Extra details report (Figure 2). When the estimation procedure fails, a red triangle will be present next to the information criteria value. Hover over the triangle to see a detailed error message.

Figure 2. . The error message shows up if one hovers over the colored triangle.

In many cases, estimation failure is due to low expression. This is the case for Figure 2 where an ANOVA model was used and the mean and maximum expression for the gene TDO2 are all equal to 1, implying TDO2 expression values are equal to 1. This is a corner case that ANOVA cannot handle.

Sometimes the estimation results are not missing but the reported values look inadequate. If this is the case, the Extra details report may show that the estimation procedure generated a warning, and the triangle is yellow. To remove suspicious results in the report, set Use only reliable estimation results to Yes in the Advanced Options (Figure 3). The warnings will then be treated the same way as estimation failures.

Figure 3. If only reliable results are used, features with warnings are not reported.

To see the results for as many features as possible, regardless of how reliable they are, set Use only reliable estimation results to No and the result will be reported unless there is an estimation failure. For example, DESeq2 uses Cook’s distances to flag features with outlying expression values and if “Use reliable results” is set to Yes (Figure 3) the p-values for such features are not reported which may lead to some missing values in the report (set Use only reliable estimation results to No to avoid this). 

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