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Several approaches for integrating microarray measurements with network knowledge were described in the literature.
The same methodology was followed to analyze the extreme values, i.e., 1% of the microarray measurements with the highest absolute values.
By comparison the Pearson correlations for the microarray measurements with TaqMan for these same 217 genes were Affymetrix (0.75), Agilent (0.80), and Illumina (0.73).
However, these datasets have dramatic target gene variances, the studies compare microarray measurements with those from PCR- and branched-DNA-based technologies that may introduce bias in amplification or detection steps, and their analyses mainly address differential expression discovery rather than global properties of the microarray.
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Single chips were used to measure the expression of 45 genes in 18 different adult and fetal tissues, and the results were compared both with microarray measurements and with conventional RT-qPCR. Figure 1A shows a picture of the microfluidic chip used in this study, a 48.48 dynamic array.
The microarray measurements were compared with quantitative real-time-polymerase chain reaction (QRT-PCR) results for 23 genes, and the varying degrees of agreement for each platform were characterized.
Microarray measurements were confirmed with real-time quantitative polymerase chain reaction (qPCR).
Moreover, T. cruzi oligonucleotide microarray measurements largely agree with known protein expression data for key functional groups.
Microarray measurements generally correlate with relative RNA molecule counts within optimal ranges but suffer from expression-dependent accuracy bias and precision that varies across datasets.
We collect six cancer prognosis studies with microarray measurements.
Overall, we found that qRT-PCR methods can give higher expression ratios as compared with microarray measurements, as reported previously [ 30].
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