AffyRegress(AffyExpress)
AffyRegress()所属R语言包：AffyExpress
Select differentially expressed genes, and output the result to a html file
选择差异表达的基因，结果输出到一个HTML文件
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This is a wrapper function complete the following tasks: 1. Create a design matrix 2. Create a contrast 3. Run regression 4. Select differentaly expressed gene 5. Output the differentally expressed gene to a html file
这是一个包装函数完成以下任务：1。创建一个设计矩阵2。创建一个对比3。运行回归4。选择differentaly表达基因5。一个HTML文件输出differentally表达基因
用法----------Usage----------
AffyRegress(normal.data, cov, compare1, compare2, method,
int=NULL, level=NULL, adj="none", p.value=0.05, m.value=0,
filename="result")
参数----------Arguments----------
参数：normal.data
an 'ExpressionSet'
ExpressionSet“
参数：cov
a list of 1-n covariates
1-N共变量列表
参数：compare1
the first value of the main covariate. For example, suppose that the main covariate is drug, and there are three unique values: "drug1", "drug2", and "placebo". You would like to compare "drug1" to "drug2". Then you would use "drug1" as compare1
主要协变量的第一个值。例如，假设，主要协变量是药物，并有三个独特的价值观：“drug1”，“drug2”，“安慰剂”。您想比较“drug1”为“drug2”的。那么你可以使用作为比较1“drug1”
参数：compare2
the second value of the main covariate. Based on the previoius example, if you would like to compare "drug1" vs "drug2", then you would use "drug2" as compare2
主要协变量的第二个值。基于previoius例如，如果你想比较的“drug1”VS“drug2”，然后你会使用捕捉“drug2”
参数：method
Three methods are supported by this function: "L" for using LIMMA method - compute moderated t-statistics and log-odds of differential expression by empirical Bayes shrinkage of the standard errors towards a common value; "F" for using ordinary linear regression; "P" for permuation test by resampling the phenotype
三种方法都支持这个功能：“L”的使用LIMMA方法 - 计算朝着一个共同的价值标准错误的经验Bayes收缩放缓t-统计量和差异表达的log赔率的“F”，使用普通的线性回归;“P”字为重采样的表型permuation测试
参数：int
if int=NULL, the interaction effect is not considered; otherwise, use two integers to indicate which covariates are considered for interaction effect. For example, if cov<-c("estrogen","drug","time") and you are considering the interaction between "estrogen" and "time", then you would write int=c(1,3)
如果INT = NULL，互动效应不考虑，否则，使用两个整数来表示协变量交互效应考虑的。例如，如果覆盖<C（“雌激素”，“毒品”，“时间”），你正在考虑的“雌激素”和“时间”之间的相互作用，那么你会写int = C（1 3）
参数：level
you only specify this term when the design matrix contains an interaction term. Suppose that you would like to compare "drug1" to "drug2" only when estrogen is "present", where "present" is one of the values of the estrogen variable. You will use "present" as level.
你只指定这个词时设计矩阵包含一个交互项。假如你想比较的“drug1”“drug2”只有当雌激素是“礼物”，“礼物”是雌激素的变量的值之一。您将使用水平作为“礼物”。
参数：adj
adjustment method for multiple comparison test, including "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". The default value is "none". Type help(p.adjust) for more detail.
多次对比试验，其中包括“冬青”，“hochberg”，“HOMMEL”，“邦弗朗尼”，“波黑”，“”，“FDR”，“无”的调整方法。默认值是“没有”。键入help（p.adjust）的更多细节。
参数：p.value
p value, the default value is 0.05
p值，默认值是0.05
参数：m.value
fold change cut-off value, default value is 0
倍cut-off值，默认值是0
参数：filename
name of the output file
输出文件的名称
值----------Value----------
A dataframe which has the same format as the one created by select.sig.gene function.
一个dataframe由select.sig.gene功能创建一个具有相同的格式。
作者（S）----------Author(s)----------
Xiwei Wu <a href="mailto:xwu@coh.org">xwu@coh.org</a>, Xuejun Arthur Li <a href="mailto:xueli@coh.org">xueli@coh.org</a>
举例----------Examples----------
data(testData)
normaldata<-pre.process("rma",testData)
result<-AffyRegress(normaldata, "group", "A", "C", "L")
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
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发表于 2012-2-25 11:14:52
