Finalizing the Quality Control

There are still various things that can be done to investigate the quality of the data but just a few final thoughts are mentioned down below.

New comparisons

As outlook, one can fit a group comparison in the app ‘New comparisons’, tab ‘New comparison’ with relevant groups, such as TB_subjects against control. If important genes are up/downregulated, then this is another sanity check that can be done.

Reporting on the quality

If there are multiple studies, one could present as follows:

• general setup of the study, things that are noticeable immediately (samples missing)
• general QC stats
• clustering
• variables that are relevant and should be/should not be
• New comparison between important groups, i.e. treatment vs control
• short summary of the study, the QC and important conclusions
• general setup of the next study
• comparison of all studies
• Slide with table: study | sample | reason to take out