The RNAseq and Microarray (Here Affymetrix U219) based gene expression are well correlated(R=0.62~0.75), which is accordance with reports by other studies. you can check "Correlation_between_RNAseq_and_U219_array_expression.pdf" for detailed correlation information of PDX models. Download: Correlation_between_RNAseq_and_U219_array_expression.pdf RNA-seq An assessment of technical reproducibility and comparison with gene expression arrays.pdf
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It is difficult to identify whether the gene was wt or just the mutation was not detected, unless the gene was covered by enough reads on each of its bases. In the Hubase, we added one column of COVRATIO in the mutation search result: COVRATIO= (The number of bases that was covered by at least 5 reads) / (The total number of bases in the transcript) * 100%. If the covratio=100, it means that all the bases in the transcript was covered by at least 5 reads, if no mutation was found, we may say the gene was wt. For the genes with covratio<100, we are not able to make sure it is wt or not. But the bigger the covratio, the more likely the gene was wt if no mutation was not found in this gene.