Joint modeling and registration of cell populations in cohorts of high-dimensional flow cytometric data.
Joint modeling and registration of cell populations in cohorts of high-dimensional flow cytometric data.
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DOI：
10.1371/journal.pone.0100334
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
McLachlan GJ
中科院分区：
文献类型：
--
作者：
Pyne S;Lee SX;Wang K;Irish J;Tamayo P;Nazaire MD;Duong T;Ng SK;Hafler D;Levy R;Nolan GP;Mesirov J;McLachlan GJ
在生物医学应用中，实验者会遇到不同的数据变化的潜在来源，例如单个样品，多个实验条件和一组标记物的多变量响应，例如来自信号网络。在常用于分析患者样本的多参数细胞术中，此类问题至关重要。虽然计算方法可以识别单个样品中的细胞群体，但没有在样品之间自动匹配它们的能力，但是难以比较和表征典型实验中的群体，例如响应于各种刺激或特定患者或时间点的区别的那些，特别是当存在许多样品时。联合聚类和匹配（JCM）是一个多层次的框架，用于跨队列同时建模和登记人口。JCM用稳健的多变量概率分布对每个群体进行建模。同时，JCM拟合一个随机效应模型来构建一个整体批量模板-用于注册样本中的人群，并对新样本进行分类。通过解决系统级变化，JCM支持涉及大型队列的实际生物医学应用。用于拟合JCM模型的软件已经在可从http://www.maths.uq.edu.au/~gjm/mix_soft/EMMIX-JCM/获得的R包EMMIX-JCM中实现。
In biomedical applications, an experimenter encounters different potential sources of variation in data such as individual samples, multiple experimental conditions, and multivariate responses of a panel of markers such as from a signaling network. In multiparametric cytometry, which is often used for analyzing patient samples, such issues are critical. While computational methods can identify cell populations in individual samples, without the ability to automatically match them across samples, it is difficult to compare and characterize the populations in typical experiments, such as those responding to various stimulations or distinctive of particular patients or time-points, especially when there are many samples. Joint Clustering and Matching (JCM) is a multi-level framework for simultaneous modeling and registration of populations across a cohort. JCM models every population with a robust multivariate probability distribution. Simultaneously, JCM fits a random-effects model to construct an overall batch template – used for registering populations across samples, and classifying new samples. By tackling systems-level variation, JCM supports practical biomedical applications involving large cohorts. Software for fitting the JCM models have been implemented in an R package EMMIX-JCM, available from http://www.maths.uq.edu.au/~gjm/mix_soft/EMMIX-JCM/.
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DOI：
10.1126/science.1198704
发表时间：
2011-05-06
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Bendall SC;Simonds EF;Qiu P;Amir el-AD;Krutzik PO;Finck R;Bruggner RV;Melamed R;Trejo A;Ornatsky OI;Balderas RS;Plevritis SK;Sachs K;Pe'er D;Tanner SD;Nolan GP
通讯作者：
Nolan GP
影响因子：
48
作者：
Aghaeepour N;Finak G;FlowCAP Consortium;DREAM Consortium;Hoos H;Mosmann TR;Brinkman R;Gottardo R;Scheuermann RH
通讯作者：
Scheuermann RH
DOI：
10.1002/cyto.990130311
发表时间：
1992-01-01
期刊：
CYTOMETRY
影响因子：
--
作者：
DEMERS, S;KIM, J;LEGENDRE, L
通讯作者：
LEGENDRE, L
DOI：
10.1073/pnas.0706409104
发表时间：
2007-11-20
影响因子：
11.1
作者：
Maier, Lisa M.;Anderson, David E.;Hafler, David A.
通讯作者：
Hafler, David A.
影响因子：
50.3
作者：
Kotecha N;Flores NJ;Irish JM;Simonds EF;Sakai DS;Archambeault S;Diaz-Flores E;Coram M;Shannon KM;Nolan GP;Loh ML
通讯作者：
Loh ML