Gilchrist_2021 QC report
- PCA of gene expression data
- MDS of gene expression data
- Expression of sex-specific genes
- Assign genotyped individuals to populations
## Number of samples in study before quality control: 264## Number of samples in study after quality control: 247PCA of gene expression data
Performs principal component analysis (PCA) of gene expression data
## Registered S3 method overwritten by 'openssl':
## method from
## print.bytes Rcpp## Setting options('download.file.method.GEOquery'='auto')## Setting options('GEOquery.inmemory.gpl'=FALSE)## Perform quantile normalization ...## Number of phenotypes: 31501
MDS of gene expression data
Performs Multi-dimensional scaling (MDS) of gene expression data using isoMDS() R function.
dist = cor(matrix, method = “pearson”)
Data are scaled to k = 2 dimensions with isoMDS(1-dist, k=2)
## Number of probes included in the analysis: 31501
Expression of sex-specific genes
Compares the expression of genes on the Y chromosome against the expression of XIST on the X chromosome to check if genetic sex has been correctly described in sample metadata. Inspired by the analysis peformed in ’t Hoen et al, 2013.
Assign genotyped individuals to populations
Project genotyped individuals to the first two principal components of the 1000 Genomes Phase 3 reference panel.
## Number of genotyped individuals in the current study Gilchrist_2021: 432## Number of genotyped individuals in the reference panel: 2157