The abundance of transcript isoforms including or excluding the cassette exons was normalized based on that of constitutive exons.
Spots with a mean intensity below their local background were excluded and the normalized M value for missing values was set to zero.
We considered each subset of the data that consisted of one genotype and one season and excluded from the normalized expression dataset genes for which we detected no read for more than 40 samples in any of these subsets, which reduced the dataset to 22,144 expressed genes.
After excluding the spots flagged for bad quality, normalized Cy5/Cy3 ratios of these loci were calculated by GenePix Pro 6.0 [ 38].
Briefly, they were baseline-corrected and normalized according to their total ion current, excluding the top 5% of intensity values to avoid bias by highly abundant species.
Well, excluding the Barrier Kult.
To exclude the possibility that normalized H-threshold values might be distorted by a difference in the distribution of the M-thresholds, H-threshold current values were also expressed using a half-maximal M-wave as unity.
* Age as of 01 Jan 2003 displayed as mean ± standard deviation (SD) † Diagnostic Cost Group (DCG) Condition Categories (CCs), excluding AD. ‡ Prospective Relative Risk Score (RRS) excluding AD, normalized to 1.0 for the eligible study population.
However, a normal or high SvO2 level does not necessarily indicate that oxygen metabolism is entirely normalized and does not exclude the presence of persisting tissue hypoxia.
For these excluded genes, we verified that their expression is higher than ten normalized RNA-seq reads per kb at other nondevelopmental time points, to exclude the possibility that they are nonfunctional pseudogenes.
Data were normalized using Block Lowess method and then analyzed at two levels of stringency (one with no data excluded; the second, data excluded when "Quality less than 1; Confidence less than 0.4; PON Ch1 or Ch2 less than 0.6").
