runningJetta(oneChannelGUI)
runningJetta()所属R语言包:oneChannelGUI
graphical interface to MADS/jetta R library.
图形界面的MADS /捷达R库。
译者:生物统计家园网 机器人LoveR
描述----------Description----------
MADS, which stands for Microarray Analysis of Differential Splicing, is a tool to identify differential alternative splicing by exon array. The principle of MADS is to increase the precision of exon-level and gene-level expression estimates by correcting, as much as possible, noise in observed probe intensities due to background and cross-hybridization. MADS incorporates a series of novel algorithms motivated by the probe-rich design of exon-tiling arrays, such as background correction, iterative probe selection and removal of sequence-specific cross-hybridization to off-target transcripts. MADS was published in RNA,2008,14(8): 1470-1479. Junction and Exon array Toolkit for Transcriptome Analysis (JETTA) is compacted version of MADS.
的MADS,差异剪接的微阵列分析,是一种工具,以确定由外显子阵列差剪接。原则的MADS是纠正以增加外显子水平和基因水平表达估计的精度,尽可能,由于背景和交叉杂交中观察到的探针强度的噪声。植物MADS采用了一系列出于切片外显子阵列的探针,如背景校正,丰富的设计新颖的算法,迭代探针的选择和删除序列特异性交叉杂交,以脱靶成绩单。 RNA,2008,14(8):1470年至1479年出版的MADS。转录分析(捷达)的交界处,外显子阵列工具包被压缩的MADS版本。
用法----------Usage----------
runningJetta()
Details
详情----------Details----------
Expression indexes are calculated as the order of Background Correction, Normalization and Summarization. In the Summarization step, background corrected and normalized probe intensities of a meta probeset are summarized to expression of the meta probeset. Meta probesets can be defined as gene/transcript clust/exon level.
作为背景校正,规范化和总结的顺序计算表达式索引。在总结步骤,背景纠正和总结荟萃probeset归探针强度元probeset表达。元的probesets可以被定义为基因/谈话的clust /外显子水平。
Background Correction JETTA estimates background signal using background probes and subtracts it from the probe intensity. If the probe intensity is less than the estimated background signal, the background subtracted signal is truncated to 1. Estimation of background signal is based on several models: Median GC: median of background probe signal of the same GC counts MAT: linear model of probe sequence with 80 parameters. see Kapur et al, 2007
背景校正捷达估计背景信号背景探测和减去探针力度。如果探针强度小于估计的背景信号,被截断的背景信号中减去1。背景信号的估计是基于以下几个型号:气相色谱中位数:80参数:探针序列的线性模型的背景相同的GC计数太探针信号的位数。卡普尔等人,2007
Normalization Normalization of JETTA is done for core probes defined in probeset annotation file. If the PSA file is not specified, it considers all probes in the MPS files as core probes. Median scaling: scaling each array so that its median is 100 Quantile: all probes of the same signal quantile have the same signal
捷达的标准化,规范化为核心探针在probeset注释文件中定义。如果PSA文件没有被指定,它认为所有探针为核心探测的MPS文件。中位数缩放:缩放每个阵列,所以,它的中位数是100位数相同的信号分量的所有探针具有相同的信号
Summarization LiWong model: multiplication model of expression and probe effect, see Li and Wong, 2001 Probe selection: select probes based on cross-array correlation of signal. see Xing et al, 2006 Median-polish
的综述LiWong模型:乘法模型的表达和探测效果,见李和黄,2001探针选择:基于跨阵列信号相关的选择探针。见兴等,2006年中位抛光
Alternative Splicing Detection Detecting alternatively expressed PSR/Exon between two sample groups based on background corrected and normalized probe intensities. It has several criteria to filter out transcript clusts and probes from the analysis. TC expression level: excluding low-expressed transcript clusts TC expression fold change: excluding transcript clusts which have big fold change between two groups Extreme probe signal: excluding probes of which signal is extremely high Cross-hybridized probes: excluding cross hybridized probes, currently pre-calculated results are needed
基于背景校正和归一探针强度的两个样本组也表示的PSR /外显子剪接检测,检测。它有几个标准,筛选出分析的成绩单clusts和探针。 TC的表达水平:低表达的的成绩单clusts训练班倍表达变化除外:不包括成绩单clusts其中有两组极端探针信号倍大变化:不包括探针,其中的信号是非常高的交叉杂交探针:不包括交叉杂交探针,目前预需要的计算结果
作者(S)----------Author(s)----------
jseok@stanford.edu
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注:
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