The deviation of the line from zero revealed a need for normalization, so prior to data analyses we normalized signals using a locally weighted scatterplot-smoothing regression (LOWESS) algorithm implemented in BASE.
Given estimates {ĥ ib } b, all probe signals can be normalized as: (6) where denotes the offset and crosstalk calibrated and probe-sequence normalized signals.
The reproducibility of the experiments was assessed by calculating Pearson's correlation of the natural logarithm of spatially normalized signals.
These corrected, normalized signals can then be used to estimate the relative abundance of particular transcripts.
To identify genes with putatively stable expression levels, normalized signals from all hybridizations of the 8 × 15 k microarray data except those from the technical replications were used to calculate a coefficient of variation (CV = SD/mean) for each gene.
The values corresponding to the western-blot signals were normalized to the total amount of histones loaded, and the ratios between the normalized signals in wild-type and PRMT1/PRMT6 knockdown cells or PRMT6 overexpressing cells, respectively, were calculated.
Normalized signals that were generated using a quantile normalization strategy (RMAExpress[25]) were used for class comparisons (ANOVA) and class predictions (BRB Array Tools; http://linus.nci.nih.gov/BRB-ArrayTools.html).html
In Fig. 1a, the expression of the selected transcripts at the different time points is plotted by normalized signals from the microarray (grey bars), together with their relative expression after normalization by GAPDH (black bars) in RT-qPCR.
On the other hand, normalized signals have the same unit variance.
This method was also used to illustrate different ventilation and gas transfer patterns in a patient with emphysema and one with pulmonary arterial hypertension (PAH .In the healthy reference cohort, the mean normalized signals were 0.51 ± 0.19 for ventilation, 4.9 ± 1.5 x 10-3 for barrier uptake and 2.6 ± 1.0 × 10-3 foRBCBC (transfer).
Scatter plots were made from normalized signals.
