Normalization was also important because the array results were compared in a cross-sample manner.
In order to calculate the gene expression ratios in a cross-sample manner, we wanted to avoid negative signals in the microarray scans.
In the present study, we analyzed the glycan-related gene expression profiles for possible correlations with cellular glycan expression profiles in a cross-sample manner, using Pearson's correlation coefficient.
By analyzing the correlation between the expression profiles for sialic acid (Sia) metabolism-related genes and the expression profiles for the GL7 epitope in a cross-sample manner, we showed that this type of correlation analysis was useful in screening for genes involved in the biosynthesis of the glycan epitope.
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In summary, our description of TUF represents the important recognition of a phenomenon relevant to many regions of the genome, thus impacting in a sample dependant manner the conduct of genome-wide studies of distinct types of genetic variation in relation to human diseases/traits.
Additional reference patterns can be incorporated to account for common sources of false positives in a sample-dependent manner.
Step measures indicate the structure of the category probability curves in as sample-independent manner as possible.
Technical variability at the library preparation, capture and sequencing creates noise that affects the numbers of reads matching to particular exons in a sample-specific manner.
Importantly, the observed differences in chromosome-specific noise-threshold values in AA versus TCGA CRC datasets (Figs. 1 and 2) further highlight ENVE's ability to model noise in a platform- and sample-agnostic manner.
Unlike other studies that have previously predicted metabolic vulnerabilities using a theoretical model of cancer metabolism, here we interpreted all datasets in a sample-specific manner (Folger et al., 2011).
