In order to correlate changes in expression level of each transcript with changes in the clinical values, we calculated, expression levels and clinical values as (value post – value pre)/value pre, and the mean for all subjects was expressed as percent change.
The calculated expression values and original probe intensity files have been deposited in NCBI'S GEO microarray database (series accession #GSE6992).
For this, the normalized and fold change calculated expression values for the Vitis and X. fastidiosa interactions experiments were mapped on to these pathways.
First, we calculated expression divergence between human and rat homologous tissues.
For each branch, we calculated expression divergence for individual tissues and jointly for all tissues (see Pairwise Expression Divergence), and summed the values from all external and internal branches.
One method was based on the LOX program that calculates expression ratios and Bayesian credible intervals and P-values for differential expression [ 45].
I revisited this question using well-established and normalized gene expression data (Faith et al. 2008) to calculate expression plasticity and found that overall correlation between noise and plasticity is weak but highly significant (rho = 0.14; P = 8E−8).
RSEM calculates expression levels and computes three different expression values: expected counts, transcripts per million (TPM), and FPKM.
The cuffdiff tool from the cufflinks package (version 2.0.2; [ 18]) was run with default parameters to calculate expression changes and associated q-values (False Discovery Rate adjusted p-values) for each gene, between the samples S1 and water, and S3 and S1.
First, Banerjee and Zhang (2003) [ 6] integrated ChIP-chip data and gene expression data to calculate expression correlation score and designed a model to assess the significance of the TF cooperativity based on multivariate hypergeometric distribution.
Afterwards, quantile scaling and WPP algorithm were used to normalize and calculate expression estimates [29].
