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Consequently, the data are organized in a phylogenetic tree in which the branch lengths represent the degree of similarity between the expression values.
We also calculated the angle between the expression values and the log expression values as an alternative measure of expression divergence and obtained very similar results (results not presented).
These are based on the frequency of probe sets with Detection call 'Absent' or 'Present' and their associated averaged values in each sample, as well as on the ratios between the expression values for 3' and 5' end of Gapdh and Actin transcripts.
We calculated Spearman's rho values to describe the degree of correlation between the expression values.
A clear correlation was observed between the expression values of both analyses for all three genes.
Strong correlations exist between the expression values derived from RNA-Seq analysis and microarray data or qRT-PCR results.
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For each cDNA sample the ratio between the expression value of the gene of interest and the expression value of B2M was calculated.
The first term in Equation (1) refers to the differential expression, while the second one combines the normalized difference between the expression value and the gene-specific threshold.
We examined the relationship between the expression value of each detected gene and the natural increase rate (NIR) of chicken body mass (Δg/g per day).
The correlation was analyzed between PFS and the expression values of PSKH1, TLK2 and PHKG2.
For each gene we calculated the log ratio of the expression values between the two transcripts across all the samples.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com