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However, the relatively high concordance achieved in this benchmark investigation is only the beginning of exploring cross-platform consistency because it is based on two microarray datasets generated on identical biological samples using different platforms, i.e., this investigation is mainly focused on a technical platform comparison.
For this, we used two microarray datasets generated for the study of Alzheimer Disease ADD).
These expression profiles have been selected from 131 microarray datasets generated at different laboratories.
Microarray datasets generated in this study have been submitted in MIAME-compliant format to the EBI database [ 14].
Affymetrix Populus microarray datasets generated in our laboratory [ 24] were used to investigate BAHD gene expression across genotypes, tissues, and stress treatments.
In order to assess the potential of NIMOO to model true biological systems we have used two microarray datasets generated in our laboratory.
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It is important to note that our approach is applicable to any microarray dataset generated from homogenous groups of samples hybridized to the arrays.
In this study, we used a microarray dataset generated in earlier work [5] to identify cyclic genes associated with the mouse segmentation clock.
We applied ARSER to analyze a real microarray dataset generated from the work of Edwards et al. (2006) in the study of the Arabidopsis circadian system.
A multi-cancer microarray dataset generated by Ramaswamy et al., and consisting of 218 tumour samples, spanning 14 common tumour types, and 90 normal tissue samples and profiled on Affymetrix oligonucleotide microarrays (Hu6800 and Hu35KsubA GeneChips).
The laser captured microarray dataset generated by Liang et al. included the microarray data of 6 regions - entorhinal cortex (EC), hippocampus (HIP), middle temporal gyrus (MTG), superior frontal gyrus (SFG), posterior visual cortex (PVC) and posterior cingulate cortex (PCC) [ 1].
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