Harshlight: a "corrective make-up" program for microarray chips.
Harshlight: a "corrective make-up" program for microarray chips.
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Harshlight：用于微阵列芯片的“矫正化妆”程序。
DOI：
10.1186/1471-2105-6-294
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发表时间：
2005-12-10
影响因子：
3
通讯作者：
Magnasco, MO
中科院分区：
文献类型：
--
作者：
Suárez-Fariñas, M;Pellegrino, M;Wittkowski, KM;Magnasco, MO
显微镜专家熟悉由于灰尘和碎片、玻璃缺陷、流体分布不均匀或表面涂层等原因导致的荧光图像可能存在的许多瑕疵。微阵列扫描确实显示了类似的伪影，这可能会影响后续分析。虽然肉眼很难发现除了最明显的瑕疵之外的所有瑕疵，特别是在高密度寡核苷酸阵列(HDONAs)中，但几乎没有工具可以帮助检测这些瑕疵。我们开发了一种新的工具Harshlight，用于自动检测和掩蔽HDONA微阵列芯片中的缺陷。Harshlight使用统计和图像处理方法的组合来识别三种不同类型的缺陷：影响少数探头的局部缺陷、影响较大区域的扩散缺陷以及可能使整个芯片失效的扩展缺陷。我们展示了Harshlight的使用可以大大改进HDONA芯片的分析，特别是对于样品之间有细微变化的实验。对于广泛使用的MAS5算法，我们表明紧凑的缺陷导致每个芯片上平均8个基因表达值变化超过50%，其中两个变化超过两倍；我们的掩蔽算法恢复了大约三分之二的损伤。成功地检测并消除了大规模伪影。
Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans do show similar artifacts, which might affect subsequent analysis. Although all but the starkest blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs), few tools are available to help with the detection of those defects. We develop a novel tool, Harshlight, for the automatic detection and masking of blemishes in HDONA microarray chips. Harshlight uses a combination of statistic and image processing methods to identify three different types of defects: localized blemishes affecting a few probes, diffuse defects affecting larger areas, and extended defects which may invalidate an entire chip. We demonstrate the use of Harshlight can materially improve analysis of HDONA chips, especially for experiments with subtle changes between samples. For the widely used MAS5 algorithm, we show that compact blemishes cause an average of 8 gene expression values per chip to change by more than 50%, two of them by more than twofold; our masking algorithm restores about two thirds of this damage. Large-scale artifacts are successfully detected and eliminated.
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DOI：
10.1073/pnas.011404098
发表时间：
2001-01-02
影响因子：
11.1
作者：
Li, C;Wong, WH
通讯作者：
Wong, WH
影响因子：
3
作者：
Suárez-Fariñas, M;Haider, A;Wittkowski, KM
通讯作者：
Wittkowski, KM
影响因子：
2
作者：
Wittkowski, KM;Lee, E;Krueger, JG
通讯作者：
Krueger, JG
影响因子：
5.8
作者：
Cope, LM;Irizarry, RA;Speed, TP
通讯作者：
Speed, TP
DOI：
10.1198/016214504000000683
发表时间：
2004-12-01
影响因子：
3.7
作者：
Wu, ZJ;Irizarry, RA;Spencer, F
通讯作者：
Spencer, F