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The best RIL populations in many species contain 200 400 RILs and these are often grown and measured in multiple replicates for the purpose of QTL analysis.
Table 1 shows two representative genes with multiple replicates for the expression ratios of Fum/O2.
The software CLUMPP [ 69] was used to align multiple replicates for K and the DISTRUCT application [ 70] was used to display the results graphically.
Linear regression with repeated measures was used to analyse IRGM expression (as estimated by ΔCt values from Q-RT PCR) with multiple replicates for each individual.
Only 16 of the 20 focal species had multiple replicates for all three neighbour treatments, and these were included in the analysis.
Sometimes multiple replicates for a factor were submitted but only one scored poorly, so we also compiled a second set of ChIP-seq experiments that only included the best available replicate for each factor and condition.
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Estimates of precision for PFOA were generally within ±10% for multiple replicates of individual samples over the range of 0.5 40 ng/mL with a more precise relative precision measure of approximately 1% for highly fortified (10,000 ng/mL) samples.
This particular CIM mapping program was chosen as it has provision for appropriate analysis of multiple replicates of each line and for multiple environments (+UV-B and -UV-B, in our case) [ 64].
Microarray technology is evolving rapidly and the trend is towards increasingly high density arrays that are capable, in principle, of generating expression profiles for multiple replicates of entire eukaryotic genomes from single chips.
Further increases in the computational needs are brought on by the need for running multiple replicates of the models and generating reliable output summaries.
A custom designed miRNA microarray that incorporated multiple replicates of 3,098 unique probes for sheep and other mammalian miRNA was used.
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