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This study also revealed that microarray quantification based on raw fluorescence maintained correlation with the real-time qPCR quantifications down to about two copies per cell, and failed to effectively quantify nearly 50% of these transcripts.
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A microarray based on oligonucleotides complementary to individual MAPH probes would allow detection and quantification based on sequence rather than on size.
Microarray: Microarray technology is based on hybridization between the target DNA and probe DNA designed with known sequences.
Majority of the genes (~98%) were found to have a magnitude of FC within the range of ≤ 1.5, while for the remaining 2% of the genes, it was 4.7-times higher in RNA-seq than the microarray based quantification.
Nevertheless, absolute qPCR has the potential to extend gene expression analysis beyond what is possible with microarray analysis, based upon the innate capability to overcome two of the greatest limitations of microarray quantification, which are limited sensitivity and lack of absolute scale [ 4].
Accurate microarray quantification is best realized when there is a linear relationship between fluorescence and RNA concentration.
Procedures for microarray quantification, quality control of hybridization intensities, and data classification were applied to the microarray signals, as described in Methods.
Real-time PCR was performed on five ESTs representing different expression clusters to verify the accuracy of cDNA microarray quantification.
A possible source of higher variation relative to the reconstitution experiments was that microarrays and FACS based quantification were run on the same individual, but on different preparations of the bulk tissue such that variation in the cellular composition of the sectioned tissue per individual may have added to the experimental noise.
Because single-color microarray systems, in general, represent more straightforward signal-abundance relationship than two-color microarray system which based on relative quantification, we used an existing Applied Biosystem data set as a reference for binning by signal.
We detect key information of high-dimensional microarray profiles based on wavelet analysis and genetic algorithm.
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