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FAQs |
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| Q: HOW MANY SAMPLES DO I NEED IN MICROARRAY EXPERIMENTS |
| A: We recommend at least 3 replicates used in expression microarray experiment. As well, considering the individual variations, such as human tissues, the sample used for replicates should be larger. |
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Q: HOW IS CUSTOMARRAY DIFFERENT FROM SPOTTED ARRAYS? |
A: CustomArray is an in situ synthesis technology. Oligo nucleotide probes are synthesized directly on the chip. This means there are no up front costs of buying hundreds of different oligonucleotides, and making changes to chip designs and layouts is easy. |
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| Q: HOW IS CUSTOMARRAY DIFFERENT FROM OTHER IN SITU SYNTHESIS TECHNOLOGIES? |
A: CustomArray chips use electrochemical detritylation to control DNA synthesis. Electrochemical detritylation is a much more efficient method to synthesize oligonucleotides than light-based synthesis processes. This means the oligonucleotides are of the highest quality and the sensitivity of the microarray is maximized. Since physical photolithographic masks, mechanical micromirrors, or inkjet technologies are NOT involved in the process, all probes can be easily changed without extra time or costs. |
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| Q: HOW LONG DOES IT TAKE TO MAKE MY OWN CUSTOMARRAY? |
| A: After you have finalized your array design, we typically ship the finished arrays within 30 days from receipt of your order. |
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| Q: WHAT METHOD IS USED FOR QUALITY CONTROL OF CUSTOMARRAY CHIPS? |
| A: Each and every synthesized CustomArray chip is quality tested by hybridization with Cy5-labeled random 9-mer oligonucleotide targets. This hybridization is used to visualize the synthesis at every electrode as well as irregular spot morphology. All hybridization data are first analyzed automatically using rigorous statistical criteria, and then inspected visually by an independent reviewer for the final ‘pass’ or ‘fail’ decision to ensure the high quality of chips shipped to our customers. The arrays that have passed the inspection are stripped of the hybridized 9-mers, washed, and dried for shipment. |
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| Q: HOW REPRODUCIBLE ARE CUSTOMARRAY CHIPS?
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A: We hybridized 20 identical CustomArray chips with the same RNA target sample prepared from the Universal Human Reference RNA (Stratagene) and labeled with Cy3 and Cy5 according to the dual-color scheme. Our raw data (no background correction) showed the following average correlation coefficients among different pairs of 20 chips: 0.97 for the Cy3 color channel, and 0.98 for the Cy5 color channel. In total, 97% of all pair-wise correlation coefficients were over 0.95.
Each probe was synthesized in triplicate, so we estimated coefficients of variation for replicate probes on the same array. In total, less than 3% of all genes had coefficients of variation exceeding 20%.
Our arrays were hybridized with the same material labeled in Cy3 and Cy5, so we calculated a false positive discovery rate based on 2-fold change in these 20 same-versus-same comparisons. Among 247,920 ratio measurements, we observed 551 ratios equal or exceeding 2-fold, thus, only 0.22% of false positives.
Such high between- and within-array reproducibility and low false positive rate have been observed with raw data prior to background correction. Background correction and simple ‘global’ normalization bring pair-wise correlation coefficients between Cy3 and Cy5 color channels on the same chip to average 0.992 (minimum 0.985) resulting in highly consistent data(faq_fig3). |
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Figure 3. Scatter plots of 15 replicate arrays hybridized with the same material (Universal Human Reference RNA) labeled with Cy3 and Cy5. For each array, X-axis is Log2(Cy3 Intensity). Y-axis is Log2(Cy5 Intensity). Raw data has been normalized and subjected to background correction. |
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