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RSEM calculates expression levels and computes three different expression values: expected counts, transcripts per million (TPM), and FPKM.
One method was based on the LOX program that calculates expression ratios and Bayesian credible intervals and P-values for differential expression [ 45].
Instead of applying a parametric test, REST software performs randomization tests (at least 2,000 randomizations) on groupwise data and calculates expression ratios of target genes compared to a reference gene along with the P-values.
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He had a handsome face, with a cold, calculating expression.
We note that formula (74) provides us a practical method to calculate expression (72).
Afterwards, quantile scaling and WPP algorithm were used to normalize and calculate expression estimates [29].
Normalized Ct values (calculated automatically within the Applied Biosystems software RQ manager 1.2). were used to calculate expression ratios between the cocaine and control groups.
Following RMA normalization, human data were further processed to calculate expression scores adjusted for gender and batch effects as described by Gudjonsson et al. (51).
The calculated expression values and original probe intensity files have been deposited in NCBI'S GEO microarray database (series accession #GSE6992).
In order to calculate expression signals, misaligned reads were avoided.
Normalized signal intensities were used to calculate expression ratios.
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