The QA/QC checks examine
- the strand synthesis efficiency (Delta-Ct of RTC-PPC)
- the presence of genomic DNA contamination (GDC), and
- whether housekeeping genes are stable across all conditions.
If the first two checks do not meet the default thresholds consistently across all samples, and are only off by a little, we recommend proceeding with the analysis with caution. However, if one or several of the samples significantly fail these quality checks while others pass, we recommend removing the problematic samples using the “Data Editor”.
For the housekeeping genes, there are two options. If many of the housekeeping genes are unstable, we recommend using quantile normalization. If only one or two of the housekeeping genes fail, we recommend removing these housekeeping genes using the “Select options” link on the normalization page, and proceeding with delta-Ct normalization.