Q-Vals (and False Discovery Rates) Made Easy

1. Q-Vals (and False Discovery Rates) Made Easy Dennis Shasha Based on the paper "Statistical significance for genomewide studies" by John Storey and Robert Tibshirani PNAS August 5, 2003 9440-9445

2. Challenge • You test plants/patients/… in two settings (or from different populations). • You want to know which genes are differentially expressed (alternate) • You don’t want to make too many mistakes (declaring a gene to be alternate when in fact it’s null – not differentially expressed).

3. First Idea • You take p-vals of the differences in expression. • P-val(g) is the probability that if g is null, it would have a difference at least this large. • You choose a cutoff, say 0.05. • You say all genes that differ with p-val <= 0.05 are truly different. • What’s the problem?

4. Thought Experiment • Suppose that no genes are truly differentially expressed. • You will conclude that about 5% of those you called significant really are. • Your false discovery rate (number null among those predicted to be alternate/number predicted to be alternate) = 100%. • Bad.

5. A Fundamental Insight • All truly null genes (i.e. not truly differentially expressed) are equally likely to have any p-val. • That is by construction of p-val (e.g. a difference has a p-val of x% if a null gene has an x% chance of having that difference or more in the two settings)

6. What Do We Do With That? • Mixture model: imagine null genes as light blue marbles and truly different genes as red ones. • If the assay is decent, red marbles should be concentrated at the low p-values.

7. 0 …. Pval …………………………………………………1

8. Method We Can Use • We don’t of course know the colors of the marbles/we don’t know which genes are true alternates. • However, we know that null marbles are equally likely to have any p-value. • So, at the p-value where the height of the marbles levels off, we have primarily light blue marbles/null genes. • Why?

9. Flat region starts here Level of flat region 0 …. Pval …………………………………………………1

10. Answer • Because if all genes/marbles were null, the heights would be about uniform. • Provided the reds are concentrated near the low p-vals, the flat regions will be primarily light blues.

11. Example: all null • Consider the all null case. • All marbles are light blue. • False discovery rate in region to left of flat region is estimated number of white marbles (based on flat region)/number of marbles to left of flat region. • This will be close to 100%

12. Flat region starts here Level of flat region 0 …. Pval …………………………………………………1

13. Example: all non-null • Consider the all non-null case. • All marbles are red and they are highly skewed. • Flat region is essentially zero. • False discovery rate in region to left of flat region is estimated number of white marbles (based on flat region)/number of marbles to left of flat region. • This will be close to 0.

14. Flat region starts here 0 …. Pval …………………………………………………1

15. Example: mixed case • Get a distribution of p-values. • Find flat region. • Estimate number of nulls in the left-of-flat region by extending the flat line. • This gives the false discovery rate.

16. Number of genes having pval Possible p-value threshold Flat line; base level of nulls 0 …. Pval ……………………………………………1

17. Example: mixed case • What would you estimate the false discovery rate to be in the case that we declare the entire area to the left of the possible p-value threshold to be significant? • 10%, 25%, 50%?

18. Number of genes having pval Possible p-value threshold Flat line; base level of nulls 0 …. Pval ……………………………………………1

19. Obtaining q-values from False Discovery Rate • Suppose we order genes from least p-value to greatest. • That corresponds to one of these cartesian graphs. • The q-value of a gene having p-value p is exactly the False Discovery Rate if the declared significance region had a threshold of p.

20. Number of genes having pval Q-value of a gene having this p-val is the FDR if this is the significance threshold. Flat line; base level of nulls 0 …. Pval ……………………………………………1

21. Lessons for Research • Mushy p-values (large error bars/few replicates) may force us to the far left in order to get a low False Discovery Rate. • This may eliminate genes of interest. • If testing out a gene is not too expensive, then we can accept a higher False Discovery Rate – nothing magical about 0.01.

22. Number of genes having pval Better p-values avoid loss of genes, for small FalseDiscovery Rate. Flat line; base level of nulls 0 …. Pval ……………………………………………1