Validation - ncbi/TPMCalculator GitHub Wiki

To validate our software, we calculate the Pearson correlation coefficient between TPM and FPKM for normalized expression values using RNA-Seq data of 1,256 samples from the TCGA-BRCA project. FPKM values were calculated using RSeQC.

Validation using UCSC hg19 genome annotation

Additionally, the correlation coefficient was also calculated for the raw read counts reported by TPMCalculator, HTSeq and featureCounts.

Scatter plots for the correlation coefficients calculated between HTSeq and featureCounts

Scatter plots for the correlation coefficients calculated between featureCounts and FPKM (RSeQC)

Scatter plots for the correlation coefficients calculated between HTSeq and FPKM (RSeQC)

Table S3: Correlation coefficient between TPMCalculator and the three tools for the samples with low correlation at least for one tool. Color scale: green high correlation and white low correlation

Validation using Gencode v25 genome annotation

The correlation coefficient calculated for the raw read counts reported by TPMCalculator, HTSeq and featureCounts.

Correlation plot for TPMCalculator vs RSeQC

Correlation plot for TPMCalculator vs HTSeq

Correlation plot for TPMCalculator vs featureCounts

Scatter plots for the correlation coefficients calculated between HTSeq and featureCounts

Scatter plots for the correlation coefficients calculated between featureCounts and FPKM (RSeQC)

Scatter plots for the correlation coefficients calculated between HTSeq and FPKM (RSeQC)