For the probe set-level analysis we used the full set of probe sets from the Exon Array including core and non-core probe sets.
The report includes information about noise, background and percentage of probe sets called present based on arbitrary threshold values [ 10].
For microarray analysis, background subtraction and normalization of probe set intensities were performed using the method of robust multiarray analysis (RMA) described by Irizarry et al (2003).
For statistical analysis, the background subtraction and normalization of probe set intensities were performed using the method of robust multiarray analysis (RMA) described by Irizarry et al. [ 30].
In practice, user can submit a customized reference list when the default background is inappropriate (e.g., if it is desired to use expressed probe sets as a background, while only a portion of probe sets are expressed in a typical expression profiling experiment).
The background levels and the range of percentage of probe sets called present (25 48%) were within acceptable levels as described previously [ 10].
All microarrays were examined for surface defects, grid placement, background intensity, housekeeping gene expression, and a 3':5' ratio of probe sets from genes of various lengths.
All microarrays were examined for surface defects, grid placement, background intensity, housekeeping gene expression, and a 3'∶5' ratio of probe sets from genes of various lengths.
Subsequent background adjustment, normalization of the raw data and estimation of probe sets signal intensities were done using GC-RMA method [ 74].
For example the normalization for microarray data includes background correction, normalization of signal and summarization of signal values of probe sets for a transcript.
