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In this previous study, we validated these arrays by demonstrating a high (greater than 80%) correlation between array data and our other methods (for example qPCR) of quantifying gene expression within these cells.
Four measures of concordance and discrepancy between array data and NGS data were calculated as described in Table 1.
The researchers randomly picked several viral ORFs to assess the correlation between array data and QPCR data (Fig. 3).
A gene by gene analysis of the expression relative to the reference sample revealed a high agreement between array data and QRT-PCR data (Table 4).
The comparison showed a strong correlation between array data and Q-PCR data (ESM Fig. 1), with Pearson correlation coefficients of 0.987 and 0.986 for Rosi/basal and RosiIG/IG, respectively.
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Correlation between array data from fresh and frozen PAXGene preparations from each donor was high across all samples prepared with Methods 1 (no depletion_Affymetrix), 2 (Globin PNAs_Affymetrix) or 4 (no depletion_NuGEN), with the exception of donor A using Method 1, where one of the microarray assays underperformed (Table 3).
To confirm the consistency between the array data and data collected from qRT-PCR and immunocytochemistry analyses, we examined the same panel of markers initially assessed by qRT-PCR.
The agreement between the array data and qRT-PCR analyses validates this multispecies microarray.
However, the fold-change ratio comparisons between the array data and qRT-PCR were higher when analyzed by qRT-PCR.
Correlation coefficients between expression array data and qPCR data were 0.71, 0.49, 0.81 and 0.91 (p < 0.001, for all four genes) for EFNA1, BOP1, SMAD2 and STMN3, respectively.
Regions that showed discordance between the array data and PCR validation displayed log2 signal ratios near zero, indicating that they are approximately equal parts loop and matrix.
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between plant data and
between array SNPs and
between volume data and
between array probes and
between weather data and
between training data and
between satellite data and
between helicity data and
between array platforms and
between array measurements and
between array replicates and
between array elements and
between array plates and
between array comparisons and
between health data and
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