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Exact(14)
We hypothesize that there is no bias to the left or right side in each of these parameters, showing average difference values not significantly different from zero.
To normalize the staining intensity variations between chips, the average difference values for all genes on a given chip were divided by the median of all measurements on that chip.
The average difference values were exported into JMPIN® 3.2.6 (SAS Institute , Inc.
Average difference values, representing the absolute hybridization intensities were then calculated for each probe set.
The corresponding expression values were the average difference values for each target.
The mean of average difference values for each transcript in HOC-EC and HA-EC was calculated.
Similar(46)
A gene was regarded as expressed if its signal level exceeded a conservative threshold of 75 average difference value.
We identified 46 target genes with >2-fold upregulation at 90% confidence interval and an average difference value expression over baseline greater than 50.
MAS5 labels each transcript as "present" (P), "marginal" (M) or "absent" (A) by taking into account the average difference value calculated between the perfect match (PM) and the mismatch (MM) as detailed in the Affymetrix Genechip procedure (www.Affymetrix.com).
For quantification of relative transcript abundance, the average difference value (Avg Diff) was used.
Using the Affymetrix Software Microarray Suite (MAS 5.0), each probe set was assigned an "average difference" value corresponding to the expression level of the particular gene it represented.
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