GENCORD QC report
Nurlan Kerimov
- PCA of gene expression data
- MDS of gene expression data
- Expression of sex-specific genes
- Assign genotyped individuals to populations
- Concordance between expression and genotype data
## Number of samples in study before quality control: 567## Number of samples in study after quality control: 560PCA of gene expression data
Performs principal component analysis (PCA) of gene expression data
Applies transcripts per million (TPM) normalisation
Genes with median expression below 1 TPM are filtered out
log2(matrix + 0.1) is applied
## Number of genes with [median(tpm) > 1]: 14634
MDS of gene expression data
Performs Multi-dimensional scaling (MDS) of gene expression data using isoMDS() R function.
Applies transcripts per million (TPM) normalisation
Genes with median expression below 1 TPM are filtered out
log2(matrix + 0.1) is applied
dist = cor(matrix, method = “pearson”)
Data are scaled to k = 2 dimensions with isoMDS(1-dist, k=2)
## Number of genes with [median(tpm) > 1]: 14634
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.
- Values on the scatter plot are log2(tpm+1).
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 GENCORD: 204## Number of genotyped individuals in the reference panel: 2157
Concordance between expression and genotype data
Uses QTLtools mbv (Match BAM to VCF) tool to check concordance between genotype data and genetic variants detected from the RNA-seq data.
## Number of non-matching genotypes: 0## Number of matching genotypes: 560
