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The Affymetrix system typically uses the Microarray suite (MAS) or its successor GeneChip Operating system (GCOS) to generate the gene signal values.
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Data presented in the paper was quality controlled using the Microarray Suite software (MAS 5.0).
We used the Microarray Suite (MAS) 5.0 [60] present/absent calls as a noise filter (absent in more than three samples with signal intensities less than 4.906) to remove absent and low hybridization features.
Previously known HCRT co-expressed genes were not reported in our analysis either because they were not listed within the top 100 SAM ranked candidates (NPTX2, GAL (galanin), and CART (cocaine and amphetamine regulated transcript), or expression was classified as "absent" (PDYN) using the microarray suite software (MAS) 5.0 algorithm.
Microarray data were analyzed using the Microarray Suite software (MAS) version 5.0 (Affymetrix).
We analyzed the results from the expression arrays using the MicroArray Suite 5.0, (Affymetrix).
The probe array was scanned and the data analyzed using the Microarray Suite Software (Affymetrix).
In rice callus cells, 16,000 expressed genes were identified using the microarray suite (MAS) 5.0 detection algorithm [ 48].
Signal intensities for each gene were generated using the Microarray Suite 5.0 algorithm by Affymetrix GCOS software 1.1.
The microarray data were preprocessed using the Microarray Suite, version 5.0 (MAffymetrixymetrix, Santa Clara, CA, USA) in the default configuration, and were analysed by a set of algorithms.
Briefly, data were extracted using the MicroArray Suite 5 (MAS5) algorithm and exported into MicroArray Data Portal for analysis and linking to bioinformatics resources.
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