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In all, current published methods are adjusted basic statistics methods and try to decrease the FPR in microarray analysis according to aforementioned approaches.
Samples were prepared for microarray analysis according to Affymetrix GeneChip® protocols.
Total RNA was isolated using Trizol Reagent (Invitrogen) and the mir VanaTM miRNA Isolation kit (Ambion) for mRNA and miRNA microarray analysis according to manufacturer's instructions.
Overall, a total of 59 RNA pools from 15 strains in 4 conditions were subjected to microarray analysis according to the procedures described [ 60].
Data were calculated from the calibration curve and normalized using the expression curve of a GTP binding protein (TC39426), whose mRNA presented an extremely low coefficient of variation (0.054; M value = 0.17) through microarray analysis according to [ 130].
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As projected, OLS, which requires constant variance assumption, was shown to be not suitable for the microarray data analysis according to the evaluation of the homoscedasticity with the residuals from OLS and 3(c)).
Following this approach, we selected those miRNAs, which were significantly differentially expressed between the two groups at a log2 ratio of ≥ 0.5 and ≤ −0.5 according to microarray analysis and according to qRT-PCR, resulting in 11 up-regulated and 6 down-regulated miRNAs, respectively.
Gene expression profiles for ashh2 inflorescences were compared to their wt counterparts using two-color microarrays and statistical analysis according to [53].
Based on this microarray analysis and according to the baseline and fold-change in the expression levels, four different lncRNA members (LOC84740, ENST00000498296, AL359062, and ENST00000438550) were selected to verify their expression levels via QPCR.
Based on this microarray analysis and according to the baseline and fold-change in the expression levels, four lncRNAs (LOC84740, ENST00000498296, AL359062, and ENST00000438550) were selected to validate the microarray results and to evaluate their roles as biomarkers in NPC patients.
For further analysis, according to the microarray expression data and literature, the co-expressed TFs and their target genes can be retrieved from AtPAN.
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