User: Nick

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Nick40
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Location:
United Kingdom
Last seen:
6 months ago
Joined:
3 years, 11 months ago
Email:
n********@kcl.ac.uk

Posts by Nick

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Comment: C: GWAS: how do we know we have the most appropriate model?
... Thanks for a very comprehensive answer Kevin! I really appreciate you taking the time to engage. While not wishing to gloss over a lot of the really helpful background/context, I just want to pick up on the key point that motivated my question. Let's stick with the age and age^2 question, i.e. when ...
written 6 months ago by Nick40
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GWAS: how do we know we have the most appropriate model?
... (Note: crossposted on Cross Validated [here][1]) My question is about how to know when the optimal statistical model has been selected for a GWAS. I appreciate that statistical models always provide only an approximation to a true process, and we aim to make inferences about those processes by cho ...
gwas genomic control inflation gc statistics written 6 months ago by Nick40 • updated 6 months ago by Kevin Blighe37k
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Recommended approach: gene set analysis of small transcriptome experiments?
... We have RNA-seq data for a small experiment, which compares the transcriptome of a treated vs untreated cell line (3 biological replicates for each condition, 6 samples in total). So far we have obtained lists of differentially expressed genes using DESeq. We want to perform gene set analysis to id ...
gene set analysis rna-seq enrichment analysis written 2.7 years ago by Nick40 • updated 2.7 years ago by b.nota6.2k
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Answer: A: LD pruning and other QC before association analysis ?
... These steps are necessary before PCA in order to identify the principal dimensions of genetic variation between samples, without over-weighting the contribution of groups of correlated SNPs. PCA is just one of the QC steps you should perform to prepare data for case/control association testing. It ...
written 2.7 years ago by Nick40
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Comment: C: GenomeStudio manual calling - how many SNPs?
... Thanks for your suggestions. Just so that I can interpret them in the context of a GenomeStudio project: In some projects I can appreciate that focusing on genes of interest will reduce the number of manual calls needed. However, in this case we are interested in genome-wide applications. Your o ...
written 3.3 years ago by Nick40
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GenomeStudio manual calling - how many SNPs?
... I am performing the initial genotype calling for around 2000 samples typed on the Illumina HumanOmniExpress chip (>900,000 SNPs). I have no previous experience of genotype calling so I am (broadly) following the protocol published by Guo et al (http://www.nature.com/nprot/journal/v9/n11/abs/nprot ...
genomestudio genotyping written 3.3 years ago by Nick40 • updated 3.3 years ago by vassialk190
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Is it possible to perform meta-analysis of gene-based LMM tests for a binary trait?
... Hi everyone, We have exome-chip data (disease cases and healthy controls) from three different studies. Currently, for each study I have performed group-based tests (CMC test, variable threshold test and SKAT-O) using a LMM to adjust for population structure (via a kinship matrix - tests performed ...
skat lmm burden tests meta-analysis snp written 4.0 years ago by Nick40

Latest awards to Nick

Popular Question 2.7 years ago, created a question with more than 1,000 views. For GenomeStudio manual calling - how many SNPs?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Is it possible to perform meta-analysis of gene-based LMM tests for a binary trait?
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: LD pruning and other QC before association analysis ?

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