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We then applied a loess normalization procedure within arrays to remove any systematic trends which arise from the microarray technology from the methylation measures [24].
We manually spot-checked all arrays to remove spots with irregular printing or dust on the array.
The prediction set was genotyped either with SNP arrays, to remove confounding with the quality of genotyping, or with GBS with the same x as the training set to maintain consistency.> (A4) The effect of reducing x per individual to expand the prediction set was quantified by calculating the response to selection (in units of standard genetic deviations) using the breeders' equation, e.g., [ 27].
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Since we would like to focus on the absorption enhancement due to the scattering in SiNW arrays, we divided A by 1 − R to assume that the intensity of an incident light right after entering into the SiNW array (to remove the effect of surface reflection) is 1.
Within Limma, minimum background correction and print-tip loess normalization was performed for each array to remove intensity-dependent dye bias and spatial effect.
Loess normalization was applied to each array to remove intensity dependent trends [ 37].
Normalizations using locally weighted linear regression and smooth scatter plot (Lowess) [ 31, 32] were performed for each individual array to remove intensity-dependent dye-bias.
Contigs considered to be differentially expressed were first checked against the S. mansoni genome to evaluate the validity of the probes printed on the arrays and to remove redundant contigs (i.e. different contigs which represented the same gene).
Normalization was carried out in two steps: first a print-tip loess within-array normalization to remove dye biases, then a between-array scale normalization to remove array biases [75].
Feline sera were preabsorbed with E. coli lysate prior to array staining, to remove background reactivity to E. coli proteins in the IVTT reactions.
First, we utilized " in vitro homology search array technology" to remove genes commonly expressed across molluscan eyes and estimate genes specifically expressed in the coleoid cephalopod camera eye.
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