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As is the case for many microarray platforms, we found that proper oligonucleotide design is critical.
Many microarray platforms include multiple probes for a subset of genes.
Over the past years, many microarray platforms, based on different technologies, have been developed by commercial and academic institutions.
Although we have identified spatial biases by their manifestation in the form of periodic autocorrelation, which in itself depends on microarray design, their frequency of occurrence should be constant over many microarray platforms irrespective of design.
Several of these studies have been very comprehensive encompassing many microarray platforms analyzed in both one and two colors, employing different probe types spotted both in-house and commercially, and using data from the same samples analyzed in several different laboratories.
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The Ensembl database (Hubbard et al. 2009) maintains and regularly updates a list of probeset mappings for many popular microarray platforms.
First, all publically available datasets from immune response experiments using many different microarray platforms and pathogens (Additional file 1: Table S1), including the ones for the response to PRRSV, were considered for the first global meta-analysis.
We build upon these studies and show that a highly reproducible reference sample can be created from a pool of RNAs derived from cell lines, and demonstrate that this reference samples gives good "coverage" across many diverse microarray platforms.
Because the available data sets use many different microarray platforms, we downloaded the processed gene expression data for each data set, most of which were associated with peer-reviewed publications analyzing the data.
Currently, many gene expression microarray platforms employ a dynamic hybridization method to generate repeatable and reproducible data.
For the many different types of microarray platforms, however, it is difficult to transform raw data so as to accord with any one of the existing frameworks, precluding reliable comparisons among dissimilar data sets.
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