Question: Possible normalization and transformation on GWAS data
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gravatar for Na Sed
3.0 years ago by
Na Sed280
United States
Na Sed280 wrote:

I was asked to write down a short report on possible normalization and transformation methods that can be applied on GWAS data. Since I am new at GWAS data, I have any idea about these matters and I do not know which keywords must be searched.

Could you please give me some normalization or transformation method names or introduce text, article, etc. about it?

ADD COMMENTlink written 3.0 years ago by Na Sed280
1
gravatar for natasha.sernova
3.0 years ago by
natasha.sernova3.4k
natasha.sernova3.4k wrote:

See these posts:

A: GWAS dataset: SNPs with association p-value

A: Gwas Stepwise Tutorial

Gwas Vs. Qtl Mapping?

A: I'm a new guy on GWAS data, what should I do?

and several papers below:

Effects of normalization on quantitative traits in association test

http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-415

Genome-Wide Association Study of Metabolic Traits Reveals Novel Gene-Metabolite-Disease Links

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3930510/

Genome-wide association analysis

http://www.stat-gen.org/tut/tut_analysis.html

Integration of GWAS SNPs and tissue specific expression profiling reveal discrete eQTLs for human traits in blood and brain

http://www.sciencedirect.com/science/article/pii/S0969996112000915

Rank-Based Inverse Normal Transformations are Increasingly Used, But are They Merited?

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2921808/

[ Inverse Normal Transformation Of A Quantitative Trait In Gwas

this post discussed the same paper ]

For microarrays:

https://www.researchgate.net/publication/11014612_Microarray_Data_Normalization_and_Transformation

Disease case:

Genetic associations with expression for genes implicated in GWAS studies for atherosclerotic cardiovascular disease and blood phenotypes

http://hmg.oxfordjournals.org/content/early/2013/10/08/hmg.ddt461.full

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by natasha.sernova3.4k
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