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Validation assays were performed in 68 samples used in the original microarray analyses, including 43 T (27 C and 16 N smokers), and 25 NT (18 C and 7 N smokers).
All microarray analyses including preprocessing, normalization and statistical analysis were carried out using R (R, 2007) version 2.6 and Bioconductor [ 39] version 2.1 as previously described by [ 40].
All microarray analyses, including pre-processing, normalization and statistical analysis were carried out using 'Bioconductor' packages in R programming language (version 2.15).
Nonetheless, a few genes with known gynoecium-enriched expression were characterized by MPSS that were not identified in previous microarray analyses, including three Embryo Defective and Embryo Defective-like genes.
The GEDAI platform allows straightforward sharing of microarray results and performing simple microarray analyses (including preprocessing, direct and indirect two-sample comparisons, 2 × 2 factorial and gene set enrichment analyses).
A study on microarray analyses including 62 human liver samples showed that mitochondrial alterations play a major role in the development of steatosis per se and the activation of inflammatory pathways is present at a very early stage of steatosis, even if no morphological sign of inflammation is observed [ 23].
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Microarray data analyses including GO analysis, Pathway Analysis, Path-net, Signal-net, and MicroRNA-gene network were performed (Genminix Company, Shanghai, China).
Abiotic stress treatments in tomato microarray expression analyses include 'Alethea' (1 99 v/v), drought (withholding water), heat (40 °C), salt (NaCl, 200 mM), or wounding (puncturing a disinfected fruit).
However, there remain several significant questions to answer with regard to microarray data acquisition and analyses, including the accurate determination of signal intensity, development of optimal analytical strategies and detection limit thresholds.
For microarray analyses, we included six treatments of RHT and TN1 before and after BPH infestation with three biological repeats for each treatment.
We want to point out that our microarray analyses also included a single case comparison (Case MS1 in comparison with all other cases).
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