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Multiple probes on a flexible platform allow one to test probes empirically and then select highly reactive probes for further iterative evaluation.
If one gene had multiple probes on the array, we selected the probe with the smallest ANOVA p-value to represent the gene.
(When one ORF was represented by multiple probes on the chip, we chose the vector with the highest average correlation to the other vectors).
The median value was used, if one set of RefSeqs was represented by multiple probes on the array.
Of the upregulated genes represented by multiple probes on the array, 54 showed varying expression patterns among the probes (Figure 1).
In some cases, the differential signal was identified by multiple probes on the array which were designed to identify species specific miRNA sequences, some of which differ by one or two nucleotides from the mouse sequence.
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Multiple probes for a gene (based on gene symbol) were median-merged.
However, in cases in which multiple probes existed on the chip (38% of the probes), reproducible calls (P: Present or A: Absent) improve the odds of a correct result.
BAC-level genotyping is also expected to increase the accuracy of genotyping assignments because it allows for a genotyping assignment to be made using multiple probes located on the same BAC.
The GAS5 transcript, which contains a cluster of highly conserved snoRNAs, can be interrogated with multiple probes available on Affymetrix arrays.
Another response conserved between the two outbreak isolates was the upregulation of transposase encoding genes within ISBcen9 (multiple probes were on the microarray; see BCAL0044 and BCAM2637, Table 5).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com