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The 39 bonferroni significant probes overlap 33 genes, including two genes with multiple significant probes.
Multiple significant probes for the same gene were removed from final data tables with the probe with the highest fold change being chosen.
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We also assessed whether the allelic directions for cis-eQTLs probes was the same when multiple significant cis-eQTL probes mapped within the same genes.
While analyzing our microarray data we found that multiple testing corrections yielded no statistically significant probes in the array.
For gene expression data, correlation was preserved at probe level, thus multiple significant correlations per gene may exist.
Testing for differential methylation between term and preterm individuals in 18 year samples failed to detect any significant probes after correction for multiple testing.
Amongst significant probes, different patterns were observed.
Probe sets were selected for prognostic significance using Maxstat R function (R.2.10.1 and bioconductor version 2.5) and Benjamini Hochberg multiple testing correction [ 18], yielding 22 significant probe sets in the two independent cohorts of patients with CLL (Table 1).
We found >1000 statistically significant probe sets after correction for multiple testing at 3-4 hrs, and >2000 significant probe sets at 24 hrs.
Adjusted p values are referred to using the notation q throughout and where multiple probe-sets exist for a gene the result for the most significant probe-set is reported.
Where multiple probe-sets existed for a gene we have reported the result for the most significant probe-set.
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