Sander W. Van der Laan

5 Questions 4 Answers 0 Followers

Questions related from Sander W. Van der Laan

What is currently the best practical method to analyse methylation QTLs?

Hi, I'd like to analyse Genetic-Variation-to-CpG correlations, i.e. methylation QTLs (meQTLs). Obviously the distribution of methylation (beta-value) of any one CpG-probe is not-normal and heavily...

29 December 2015 1,450 2 View

Bonferroni or FDR correction in regional eQTL analyses?

For a regional analysis of a bonafide GWAS locus I’ve got 1,717 variants associated with the expression of 12 genes in the region in 7 tissue. So I’m running 1,717 X 12 X 7 = 144,228 tests. What...

29 October 2015 5,456 5 View

If replication is practically impossible, what other (statistical) methods would help to validate and verify a (suggestive) genome-wide hit?

We've run GWAS on special traits. Unfortunately our cohort is unique in its kind. We cannot replicate. We can only validate and verify results in the context of other (related) traits or find...

27 October 2015 2,256 7 View

How do I read (interpret) the allele-coding of pharmacological variants, for example CYP2C19*2?

As usually GWAS/ExomeChip data is encoded as chr:bp or with a rsID, I'm looking for an easy method to interpret those "pharmacological variants" like CYP2C19*2.

27 October 2015 6,246 7 View

Why would you want to use "inverse normal transformation" on a trait compared to a simple log-transformation?

Often I see papers where they use "inverse normal transformation" to transform a not-normally distributed trait. I understand why you'd want to transform. But what is the advantage of using...