affyGG：用于Affymetrix芯片的遗传基因组学计算协议
affyGG: computational protocols for genetical genomics with Affymetrix arrays.
作者信息
Alberts Rudi, Vera Gonzalo, Jansen Ritsert C
机构信息
Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands.
出版信息
Bioinformatics. 2008 Feb 1;24(3):433-4. doi: 10.1093/bioinformatics/btm614. Epub 2007 Dec 16.
MOTIVATION
Affymetrix arrays use multiple probes per gene to measure mRNA abundances. Standard software takes averages over probes. Important information may be lost if polymorphisms in the mRNA affect the hybridization of individual probes.
RESULTS
We present custom software to analyze genetical genomics experiments in human, mouse and other organisms: (i) an R package providing functions for QTL analysis at the individual probe level and (ii) Perl scripts providing custom tracks in the UCSC Genome Browser to check for sequence polymorphisms in probe regions.
AVAILABILITY
动机
Affymetrix阵列使用每个基因的多个探针来测量mRNA丰度。标准软件对探针进行平均计算。如果mRNA中的多态性影响单个探针的杂交，可能会丢失重要信息。
结果
我们展示了用于分析人类、小鼠和其他生物体基因基因组学实验的定制软件：（i）一个R包，提供在单个探针水平进行QTL分析的功能；（ii）Perl脚本，在UCSC基因组浏览器中提供定制轨迹，以检查探针区域的序列多态性。
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