Thus, our conclusions (of high overlap across species), are conservative with respect to the technical batch effect.
All tissues used for downstream studies were prospectively randomized during processing and sectioning, prior to expression analysis, to minimize technical batch effects in the data.
It is remarkable that we have been able to observe this considerable conserved chromatin signature despite the obvious confounding technical batch effect in these comparative data.
Given this study design, we expect the technical batch effect to result in the appearance of inter-species differences; yet, our goal is to demonstrate similarity across species.
Second, there was a (not-recorded technical) batch effect in generating the short read sequencing data for these tumor and normal prostate samples.
We note that since different labs produced the human and chimpanzee data, we expect a considerable technical batch effect to be completely confounded with species annotation.
A comparison of patient characteristics based on phenotypic group can be found in Additional File 3. Notably, we ensured that the patient samples in the training cohort were all processed together to minimize technical batch effects.
In summary, we used the brainarray HGU133Plus2-Hs-Entrez HGU133Plus2-Hs-Entrez HGU133Plus2-Hs-Entrez 45], data were then normalized with GC-RMA [ 46], technical batch artefacts were corrected using a linear model, and genes with noise-leversionression in 95% or more arrays were filtered out leaving 13543 probesets eacustomresponding to a unique Entrez Identifier.
β j measures the strength of association between methylation levels at position j and age X i. W i,k and α k,j refer, respectively, to the covariates (e.g. technical batch effects or gender) and their corresponding regression coefficients.
