Exact(3)
Mean ratios and standard deviations (SDs) for all array elements spotted in triplicate were calculated and the datasets normalized to the median ratio per hybridization.
Processing of the TIFF images from hybridized arrays was performed using TIGR-Spotfinder http://www.tigr.org/software, and the datasets normalized by applying the LOWESS algorithm, using block mode and a smooth parameter of 0.33, available in the TIGR-MIDAS package http://www.tigr.org/software.
Because our analysis was performed on datasets normalized to 40 million reads, we set up the threshold at 8 (which represents a minimum rpbp of 1.5 for the time point with the least coverage; Rep1, ZT14, 7,497,386 sequences).
Similar(57)
Specifically, key established pathways in lung cancer exhibit higher statistical significance using a dataset normalized with our reference genes relative to normalization without using our reference genes.
where the corrected image intensity is derived from the measured raw image, by subtracting, the average image over the full large dataset, normalized by the standard deviation image of that dataset.
where the corrected image intensity is derived from the measured raw image by subtracting, the average image over the full large dataset, normalized by the standard deviation image of that dataset (dimensionless units are used throughout).
The downloaded SOHO/SEM daily EUV flux is the dataset normalized to 1 AU.
The structural (T1 – MPRAGE) and functional data were coregistered for each participant dataset, normalized into the standard Montreal Neurological Institute space, and then transformed into a common stereotactic space based on Talairach and Tournoux [28].
Results from SAM were compared using the dataset normalized by MAS 5.0 alone, versus the same dataset normalized by MAS 5.0 with scale normalization using the lung- NEPS reference genes represented on the microarray.
PCA analysis using this dataset normalized for the organ effect resolved two temporal phases of the transcriptomic response to cytokinin.
The Affymetrix U133A data files were compiled in a single dataset, normalized by MAS5, scaled to a target intensity of 600 and log2 transformed.
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