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We calculated the mean log ratio, and coefficient variation (CV) score for each group (data available upon request).
QTL mapping was performed using R/qtl [60], and testing for linkage of both clinical traits and gene expression (using the mean log ratio of the expression) was conducted using a linear model [33], [59].
The mean log ratio was calculated from the ΔΔCt (−2−ΔΔCt).
The next two columns present the bounds of the 95% confidence interval for every mean log ratio.
The distribution of relative FPKM values was evaluated using one-sided t-test against the mean log ratio of whole genes.
Cy5/Cy3 log2 ratios of background-subtracted intensities were extracted, and each array was normalised such that the mean log ratio equalled zero.
Similar(48)
ANOVA was then used to compare the mean log ratios with the Student-Newman-Keuls test to make multiple comparisons.
Segmented mean Log ratios of probe signals for UBC lines in the Cancer Cell Line Encyclopedia (http://www.broadinstitute.org/ccle/home ).org/ccle/home
We calculated the mean log ratios of all expressed genes from the tumors with concomitant CIS compared to the expression in tumors without concomitant CIS and superimposed the gene expression data to the FGF and p38/MAPK canonical pathways.
Along with this analysis, mean log ratios (weighted according to the P level of significance) of genes belonging to biosynthesis (BS), metabolism (MET), transport (TR), perception (PER), signal transduction (ST) and hormone-responsiveness (HR) categories were calculated for each of the eight hormones considered by the HORMONOMETER.
The mean log-ratio for the global data was −0.06 with a standard deviation of 0.55 (Table 2), showing a homogeneous distribution of the coverage between affected and control individuals.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com