After applying background correction, log transformation, and normalization procedures, we tested if the miRNA profile changes after chemotherapy.
If after this correction, log Cy5 signal in array differed by > 3·SD from the mean log Cy5 signal it was replaced by the mean.
Our data indicates that after correction, log ratios between measured and predicted peak intensity log (f j/ p j) roughly follow a normal distribution.
The density-correction log from the LDS tool records the absolute deviation from the measured bulk density.
Where PCT rates of a candidate explanatory variable were close to zero we used a continuity correction (log(1+p), where p is the fractional rate) to avoid potential excess influence.
Data processing and statistical analyses were done within the R statistical environment, v. 2.13.1 [ 25]. Background correction and log 2-ratio transformation were performed according to the NormExp method with offset = 50; any intensity that is less than 0.5 after background subtraction is reset to be equal to 0.5 [ 26].
For each RAR methods, the results of the following 5 test statistics are shown: Agresti's correction to Wald-type Z test T MW, log-relative-risk test T Risk, Gart's correction to log-odds-ratio test T MO, Cook's correction to chi-square test T MC, and Williams' correction log-likelihood-ratio test T ML.
To estimate the magnitude of allelic ratio correction, log-transformed allelic ratios from both correction methods (IUPAC or allele-switched) were regressed against the log-transformed allelic ratios from standard alignment.
RMA values are multi-chip model-based relative expressions of arrays via background correction, log-transformation and normalization and gene-by-gene processing with robust median polish of PM values (perfect match) [ 28- 30].
Magnetic hysteresis loops before (a, c, e, g) and after (b, d, f, h) paramagnetic correction; depth logs of low-field (i), paramagnetic (j), and ferrimagnetic susceptibilities (k); saturation magnetization (Ms) (l); and coercivity (Hc) (m) of selected samples from depths between 589.05 and 589.55 m in the WFSD-1 core.
Expression measurements were pre-processed to provide background correction, normalization and log base 2 transformation using RMA (Robust Multi-array Average) [77].
