Analysis guides
Reading your results
Which numbers to read in which order, and what not to believe.
The order to read in
- QC summary — if it fails here, the numbers below are not worth reading
- Alignment rate — tells you whether the reference genome was the right one
- PCA — whether the groups separate, and whether there is a batch effect
- Differential expression — only meaningful once the three above are sound
What QC catches
A low alignment rate (under 70%). Usually the reference genome is from a different species, or adapters were left in.
A high duplication rate. This means low library complexity, which is common when the input amount was small. The results are not unusable, but read expression levels with care.
What not to believe
Do not select on the p-value alone. Use the value after multiple-testing correction (FDR). An uncorrected p < 0.05 means about a thousand of twenty thousand genes pass by chance.
A large fold change does not make a gene important. Genes expressed at very low levels turn small changes into large ratios. Read the baseline expression alongside it.
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