Hybridization signals from multiple probes for each target strain were integrated using a novel algorithm for data analysis.
To establish a convenient, cost-effective, and reasonably reliable method for monitoring multiple gene expression using customized membrane-based macroarray, we constructed a cDNA macroarray with multiple probes for 13 human vascular endothelial genes and assessed the accuracy of the macroarray measurements.
Excluding multiple probes for single gene and unmapped probes to rice genome, 3095, 3613, 2926 and 2774 unique DEGs were identified for Nipponbare callus.
The array included multiple probes for some genes; here the strongest signal was retained and weaker ones deleted.
Expression levels were inferred using custom designed exon-junction microarrays carrying multiple probes for each transcript as described [17].
Notably, multiple probes for Gli2 and Smo were attenuated by 4.2, and 3.2-fold respectively (Table S3).
We utilized multiple probes for each pathogen (approximately 30 to 100) that were designed from conserved regions of the respective genomes.
Multiple probes for a given transcription unit render abundant measurements which allows for further statistical evaluations, and therefore, leads to more accurate results.
However, the availability of limited number of fluorescence labels that can be monitored simultaneously has hampered the use of multiple probes for multiplex assays.
When there were multiple probes for one gene, we selected the probe with the highest variance across the samples, ending up with 110 unique DASL probes.
