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Meta-analytical estimates were obtained using the "Metafor" package.
The analyses were done using the metafor package from R open-source software [20].
Meta-analytical estimates were obtained using the "Metafor" package (Viechtbauer 2010).
All other calculations and analyses were conducted in R (R Development Core Team [2011]; R Core Team [2014]) using the metafor package (Viechtbauer [2010a], [b]).
The analysis was conducted in the statistical program R using the metafor package.
Funnel plotting and Egger's linear regression test were performed using the Metafor package [ 23] in R [ 25], Version 3.0.2.
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Regression coefficients and SEs from individual replication studies were pooled using an inverse-variance-weighted fixed-effect meta-analysis, using the metafor R package (http://www.wvbauer.com/downloads.html).html
Attempts at linear modeling, performed as a meta-analysis comparing ratios from the different methods using the metafor R package [ 34], did not return the theoretically expected level of agreement between observed allelic ratios from any alignment methods when compared against SNaPshot in either cDNA synthesis method (data not shown).
A sample size-weighted z-score based meta-analysis was used to combine the gene expression data from both cohorts (n = 1977) using the metafor meta-analysis package for R, version 1.4-0 (http://www.jstatsoft.org/v36/i03/).org/v36/i03/
VW prepared the Additional files 1, 2 and 3 document that provides code that can be used with the metafor package.
R code for use with the metafor package is also provided Additional files 1, 2 and 3.
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