Exact(9)
Microarray quality was validated by the good reproducibility of experimental measurements of multiple biological and analytical replicates.
Individual microarray quality was evaluated based on QC report, pair-wise MA-plots, and box plots.
Overall microarray quality was verified by the following criteria: (1) RNA Integrity Number (RIN) >7.0; (2) 3'/5' ratio for GAPDH <3; and (3) scaling factor <10.0 [22].
Individual microarray quality was assessed using M vs A scatter plots.
CodeLink microarray quality was assessed using the CodeLink Expression analysis software v4.0.
Microarray quality was assessed by a PCA plot and the quality-control metrics implemented in Partek Genomics Suite.
Similar(51)
Four broad groups of quality indicators in gene expression profiling studies (clinical, tissue, RNA, and microarray quality) were identified.
We find that clinical, tissue, RNA, and microarray quality are all useful variables for collection and consideration in study design, analysis, and interpretation of gene expression results in human postmortem studies.
Comparable thresholds were obtained when different measures of microarray quality were used (Figure S2B).
Subjects with aneuploidy and poor microarray quality were not included, leaving a final sample size of 4,411 individuals including 415 patients with short stature, 196 patients with tall stature and 3800 patients with normal stature.
Microarray data quality was checked using diagnostic image plots and MA-plots and was found to be satisfactory.
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