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Mean transformed expression is approximately 8% greater near the terminus of chromosome 1 than at the middle of chromosome 3.
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Values represent mean of the log base 2 transformed expression data.
The proliferation score was calculated using the arithmetic mean (average) of the normalized and transformed expression of a subset of the 50 classifier genes (Additional file 10: Table S5) that are associated with cell cycle progression and which were shown to be co-regulated in the gene-associated dendrogram from the training set hierarchical cluster (Fig. 2).
For each annotated gene and in each of the two conditions (myoblasts and myotubes), the normalised mean expression was calculated from its average log2base transformed expression across the triplicate.
Expression profiles of transcription factors were clustered using log-2 transformed expression fold changes at each time point as compared to the control by k-means clustering method with MEV (version 4.6.2) [ 42].
Furthermore, standard deviations of log transformed expression ratios for each gene (for 3 or 4 replicate spots, depending on the array used), were plotted against the mean log transformed expression signals and analyzed by regression analysis.
The transformed expressions were then clustered using the fuzzy c-means (FCM) clustering algorithm in the Bioconductor Mfuzz package [ 89].
RPKM values were root mean transformed.
b Mean transformed symptom severity scores.
c Mean transformed health-related quality-of-life scores.
That could mean transforming prison cell into scholar's den".
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