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Quality assessment of expression data
The un-scaled distributions of raw intensity values provide a good indicator of how similar or dissimilar chip data are within an experiment. Box Plots of the raw intensities for each chip are a typical way of examining raw intensities. The red colored box is the range of the intensities from the middle 50% of data points. The dark black line in the colored box is the median intensity. The grey "whiskers" extending above and below the colored box indicate the overall range of the intensities.
Repeated Analysis of Stratgene Reference RNA. Five Stratagene reference RNAs were processed using PBRs automated processing and the data compared with samples processed in another laboratory. Box plots of the un-scaled brightness were then plotted (log2 scale) using the affy package in "R"( ).
The highly consistent and reproducible data from Precision Biomarker Resources indicated that technical variability is not a factor. Normalization can be kept to a minimum increasing the sensitivity of your analysis.
Reference RNA samples like the Stratagene Reference RNA provide a means for testing the performance of an assay. At Precision Biomarker Resources we regularly test our procedures to insure you are receiving the highest quality and reproducible data. The box plot figure below demonstrates the consistency of our processing over time.
Performance Testing at Precision Biomarker Resources. Stratagene Reference RNA was processed on 3 separate dates approximately one month apart and hybridized to Affymetrix U133 2.0 chips. Each number represents a different test date.
With Precision Biomarker Resources, you now have the ability to compare today’s results with tomorrow’s experiments.
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