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Briefly, normalization was performed for each array by first plotting a frequency histogram of the raw expression data for all genes.
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In [10], Hemmi describes the nonlinear PA response of an active linear array by a third-order polynomial and develops equations for the beam-pointing angle of the harmonics and intermodulation products.
The normalized volume for each spot on each array was calculated by first removing the background signal estimated by the first quartile of the nonspots, and then log-transformation of the spot volumes was used to generate normally distributed data.
These individual probe intensities are used in the subsequent preprocessing steps, during which each array is standardized by first estimating and then subtracting the background signal in order to reduce the effect of non-specific hybridization [ 44].
Probe-wise analysis of 450k arrays was performed by first adjusting for technical confounding effects; DNA methylation levels at each CpG locus were adjusted using a generalised linear model (GLM) with beta-distributed response [ 49] including microarray and position on the microarray as technical confounders.
In addition, 3 (2.2%) of the patients had embryos screened by array CGH first and then had the euploid blastocysts cryopreserved in order to avoid ovarian hyperstimulation syndrome (OHSS).
In this way, the Floquet wavenumbers of any multiple array structure can be computed by first considering the master structure alone and then computing the effect of attaching each array in turn.
High throughput gene expression analysis by real time PCR in a microfluidic dynamic array was first introduced by Spurgeon et al.[ 40], and has since been successfully applied to copy number variation studies [ 53] and quantitative miRNA expression analysis [ 54].
During the inner convolutional step, the bit array is first encoded by the convolutional encoder and then punctured by the predefined convolutional code rate.
Comparison of the ChIP-seq data with the array expression data was carried out by first performing an RMA normalisation of the mouse spermatid expression.
Confirmation of the methylation status reported by the BeadChip array for each donor was conducted by first bisulfite converting 100 ng of genomic DNA from 31 samples (21 EA; 10 AA) as described earlier in this paper.
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