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From a scatter plot of the normalized indices vs. normalised background, the false positives were identified and excluded in the analysis of the patient data.
The data were normalised, background corrected and summarised using the Robust Multichip Average algorithm implemented in the Expression Console version 1.1.2 software (Affymetrix).
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Expression data were normalised, background-corrected and summarised using the RMA algorithm, http://www.partek.com/.com/
Expression data were normalised, background-corrected, and summarised using the RNA algorithm.
Therefore, peak correction was performed using the IMA package, moreover data were normalised using background correction followed by quantile normalisation method.
Raw CEL files were processed using RMAExpress software (http://rmaexpress.bmbolstad.com) using the background-adjusted and quantile normalised setting, and intensity data was summarised using robust multiarray average (RMA) expression values.
The probe intensities were normalised for background noise with the robust multiarray average (RMA) method [27] using only perfect match (PM) probes.
Gene array signal intensities were normalised to background signal, log-transformed and rescaled to ensure each data point lay between lowest and highest signal intensity.
These shRNAs were screened in an assay in which a short 60 bp target of either the mutant or the wild-type ataxin7 gene sequence was inserted in the 3'UTR of Renilla luciferase and normalised to background Firefly luciferase (Figure 1B).
Cytolysis was quantified by lactate dehydrogenase (eBioscience) release and normalised for background values.
Data were normalised using background correction and the cubic spline method (Workman et al, 2002).
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