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As the compositions of microarrays are regularly updated to incorporate new genes with improved target sequences, it is evident that combining data from different generations of the same microarray platform will generally result in largely varying numbers of samples per gene.
However, as we discover in this work, continual changes in genomic sequence annotations and probe design criteria make it difficult to compare gene expression data even from different generations of the same microarray platform.
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The replicate data were highly consistent when the same target was hybridized to two different sectors of the same microarray chip, to different microarray chips, or to the same microarray chip upon re-use (Fig. S2A).
Application of biochip for concurrent detection of various immobilized target DNA and protein molecules and multiplex of DNA and protein on the same microarray was accomplished.
We generated the data from each mouse model using the same microarray platform and reference RNA.
However, if the same microarray is used for all species, results may differ between species because of species-specific mutations that affect the binding affinity of the probes.
Using in vivo and in vitro breast cancer microarray datasets, SplicerAV was able to perform both gene and isoform specific expression profiling within the same microarray dataset.
Despite all preprocessing, it has been shown that data generated in different labs or on different microarray platforms or on different generations of the same platform may not be comparable due to platform or lab specific biases [ 8].
Three generations of the same loving family.
Many residences include multiple generations of the same family.
These data sets were generated using different generations of the Affymetrix GeneChip oligonucleotide microarray.
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