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To determine PCR efficiency, a coefficient file was created for each target cDNA and the housekeeping control.
The standard curves were saved in a coefficient file that was used by the relative quantification software from Roche to calculate the mRNA levels relative to GAPDH.
In this experiment, the coefficient file was created by PCR amplification of hBD2 and hHPRT as the housekeeping gene in a series of diluted cDNA (relative standard curve) in triplicates.
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Undefined coefficients are marked with '-'; these should be set to 0.0 in numerical calculations as is the case in the coefficient files available online.
ACIS "dead area" coefficients file, which may have the values "NONE" (no dead area computation), CALDB (for automatic lookup), or an explicit file reference to an ACIS "dead area" coefficients FITS table.
If the exact number of visitors who downloaded the coefficients file is unknown, we learn that 10%% of them cared to visit the IGRF Healthh warning" page and showed enough interest to stay there long enough to read the recommendations.
Data of real-time PCR, including calibrator and samples, were imported into the Relative Quantification Software and analysed with the Fit Coefficients File.
For calculating texture coefficient, JCPDS file 87-0639 of Pd has been used.
Similar trends between the inter-set relationships were obtained with the DFP and the Tanimoto coefficient (Additional file 1: Table S2 and Fig. S3), and the inter-set relationships calculated with MACCS keys and the Tanimoto coefficient (Additional file 1: Fig. S4).
The correlation between RNAseq/ in silico data and qPCR data was assessed by calculating the Pearson's product moment correlation coefficient (Additional file 3: Table S1).
However, the outliers and variation in the lowly expressed genes negatively affect both the Pearson Correlation Coefficient (Additional file 1: Table S6) and identification of differentially expressed genes.
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