Assessment of the relationship between pre-chip and post-chip quality measures for Affymetrix GeneChip expression data.
Assessment of the relationship between pre-chip and post-chip quality measures for Affymetrix GeneChip expression data.
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评估Affymetrix Genechip表达数据的片前和片后质量测量之间的关系。
DOI：
10.1186/1471-2105-7-211
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发表时间：
2006-04-19
影响因子：
3
通讯作者：
Hodges, Angela K.
中科院分区：
文献类型：
--
作者：
Jones, Lesley;Goldstein, Darlene R.;Hughes, Gareth;Strand, Andrew D.;Collin, Francois;Dunnett, Stephen B.;Kooperberg, Charles;Aragaki, Aaron;Olson, James M.;Augood, Sarah J.;Faull, Richard L. M.;Luthi-Carter, Ruth;Moskvina, Valentina;Hodges, Angela K.
基因表达微阵列实验的实施成本很高，并且样品与芯片杂交之前和之后的中间步骤中可接受的质量控制指南也很模糊。我们进行了一项实验，将人脑 RNA 与 117 个 U133A Affymetrix 基因芯片杂交，并利用这些数据探索 4 个芯片前变量与 22 个芯片后结果和质量控制措施之间的关系。我们发现芯片前变量彼此显着相关，但这种相关性在 RNA 质量和 cRNA 产量测量之间最强。尸检间隔与这些变量呈负相关。反映阵列异常值、阵列调整、杂交噪声和 RNA 完整性的四个主要成分解释了大约 75% 的芯片后测量总变异性。芯片前和芯片后变量之间存在两个显着的典型相关性，源自 MAS 5.0、dChip 和 Bioconductor 软件包 affy 和 affyPLM。最强的（CANCOR 0.838，p < 0.0001）将 RNA 完整性和产量与芯片后质量控制 (QC) 测量索引 3'/5' RNA 比率、芯片的偏差或缩放以及整个芯片的信号变异性的缩放相关联。尸检间隔相对不重要。我们还发现，通过芯片后测量 B_ACTIN35、GAPDH35 和 SF 可以较好地预测 RNA 完整性数 (RIN)。我们发现，与杂交前可测量的数量具有最强关联的芯片后变量是反映 RNA 完整性的变量。我们提前确定的变量无法很好地预测质量的其他方面，例如噪声测量（反映测定的执行）或反映数据质量的测量（异常值状态和阵列调整变量）。可能存在其他可测量的预杂交变量，这些变量可能与表达数据质量测量更好地相关。发现这种连接可以通过在杂交前消除不良样本来节省昂贵的微阵列实验成本。
Gene expression microarray experiments are expensive to conduct and guidelines for acceptable quality control at intermediate steps before and after the samples are hybridised to chips are vague. We conducted an experiment hybridising RNA from human brain to 117 U133A Affymetrix GeneChips and used these data to explore the relationship between 4 pre-chip variables and 22 post-chip outcomes and quality control measures. We found that the pre-chip variables were significantly correlated with each other but that this correlation was strongest between measures of RNA quality and cRNA yield. Post-mortem interval was negatively correlated with these variables. Four principal components, reflecting array outliers, array adjustment, hybridisation noise and RNA integrity, explain about 75% of the total post-chip measure variability. Two significant canonical correlations existed between the pre-chip and post-chip variables, derived from MAS 5.0, dChip and the Bioconductor packages affy and affyPLM. The strongest (CANCOR 0.838, p < 0.0001) correlated RNA integrity and yield with post chip quality control (QC) measures indexing 3'/5' RNA ratios, bias or scaling of the chip and scaling of the variability of the signal across the chip. Post-mortem interval was relatively unimportant. We also found that the RNA integrity number (RIN) could be moderately well predicted by post-chip measures B_ACTIN35, GAPDH35 and SF. We have found that the post-chip variables having the strongest association with quantities measurable before hybridisation are those reflecting RNA integrity. Other aspects of quality, such as noise measures (reflecting the execution of the assay) or measures reflecting data quality (outlier status and array adjustment variables) are not well predicted by the variables we were able to determine ahead of time. There could be other variables measurable pre-hybridisation which may be better associated with expression data quality measures. Uncovering such connections could create savings on costly microarray experiments by eliminating poor samples before hybridisation.
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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：
14.9
作者：
Imbeaud S;Graudens E;Boulanger V;Barlet X;Zaborski P;Eveno E;Mueller O;Schroeder A;Auffray C
通讯作者：
Auffray C
影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
DOI：
10.1016/0169-328x(94)00219-5
发表时间：
1995-02-01
期刊：
MOLECULAR BRAIN RESEARCH
影响因子：
--
作者：
KINGSBURY, AE;FOSTER, OJF;MARSDEN, CD
通讯作者：
MARSDEN, CD
影响因子：
4.8
作者：
Piper, MDW;Daran-Lapujade, P;Pronk, JT
通讯作者：
Pronk, JT