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Microarrays were assessed using Affymetrix Expression Console Software 1.1 without changing the default settings (Affymetrix), and the data quality was deemed adequate for further analyses.
ER and PR status, using tissue microarrays, were assessed according to the American Society of Clinical Oncology and College of American Pathologists guidelines with cut-off value of 1% positive tumour nuclei [ 25].
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The quality and quantity of the RNA used for the microarrays was assessed using a Nanodrop spectrophotometer (Nanodrop Technologies) and 2100 Bioanalyser (Agilent Technologies).
The quality control of the microarrays was assessed using the standard Agilent controls to verify that the arrays met the expected criteria.
The miRNA expression levels of the 64 patients evaluated in the microarray were assessed using real-time PCR for relative risk analysis.
Overrepresented biological processes among the MPH-correlated genes located to the MPH-ASs in comparison to all genes from the 46k-microarray were assessed using the package topGO (version 1.10.1) in R (http://www.r-project.org) including the weight algorithm [ 48].
Sensitivity of the microarray was assessed by contamination of a cheese with an Enterococcus faecium strain carrying vanA gene.
The performance of an informative pilot microarray was assessed and identification of putative miRNAs was possible.
Reproducibility and reliability of each single microarray was assessed using Quality Control report data.
The differential expression of several genes detected by the microarray was assessed and confirmed by quantitative real-time PCR.
Total RNA integrity for microarray was assessed using RNA 6000 nano lab chip on the 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) following the manufacturer's protocol.
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