doPlotFCT(ABarray)
doPlotFCT()所属R语言包：ABarray
Calculate fold change and t test, the plot
计算倍数变化和t检验，积
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Calculate fold changes and p values from t test, and plot the results using preset FDR threshold
倍的变化，从t检验，p值计算，并绘制使用预设的FDR阈值的结果
用法----------Usage----------
doPlotFCT(eset, group, grpMember, order1 = NULL, order2 = NULL,
detectSample = 0.5, snThresh = 3, ...)
参数----------Arguments----------
参数：eset
an ExpressionSet object
ExpressionSet对象
参数：group
which group from experiment design should calculation and plot be performed
从实验设计组应进行计算和绘图
参数：grpMember
optional group member within the group
组内的可选组成员
参数：order1
optional, For a pairwise comparison the ordering of the first group of replicates
可选的，对于成对比较第一组的顺序复制
参数：order2
optional, For a pairwise comparison the ordering of the first group of replicates
可选的，对于成对比较第一组的顺序复制
参数：detectSample
optional number between 0 and 1 to indicate the percentage of arrays should be above snThresh to include in the t test analysis. Default = 0.5. If the probe is detected in 50% or more samples on one of the subgroup, the probe is included in the t test, otherwise, it will be excluded in the t test
可选0和1之间的数字表示阵列的比例应该高于snThresh包括t检验分析。默认值= 0.5。如果探针在50％或更多的样本的分组检测，探针包括t检验，否则，将被排除在t检验
参数：snThresh
optional S/N ratio threshold. Default = 3
可选S / N比阈值。默认值= 3
参数：...
Additional argument, currently not implemented
额外的参数，目前尚未实现
Details
详情----------Details----------
Group members are optional. For example, if group name is "tissue", and group members in experiment design file include "brain", "liver", "lung", "muscle". We could include c("brain", "liver") as group member for the parameter, then t test will be performed between "brain" and "liver", and "lung" "muscle" will be ignored. However, if we omit group member in the arguments, all tissue members will be used for t test. In this case, there will be 6 pairwise t test between each member of the group.
小组成员是可选的。例如，如果组的名称是“组织”，并在实验设计文件组的成员包括“大脑”，“肝”，“肺”，“肌肉”。我们可以包括c（“大脑”，“肝”）组成员为参数，然后将t检验的“大脑”和“肝”和“肺”之间进行的“肌肉”将忽略。然而，如果我们忽略的参数组的成员，所有的组织成员将使用t检验。在这种情况下，将有6成对ţ每个组的成员之间的测试。
If order1 and order2 are specified then a paired sample t-test will be conducted between the groups, with the arrays in each group sorted according to the ordering specified. For example, if order1 is c(1,3,2) and order2 is c(1,2,3), then the sample pairing is a1-b1, a3-b2, a2-b3, with a and b are subgroup 1 and subgroup 2 within the group.
配对样本t检验，如果order1和order2指定，那么将各组之间进行，每组阵列按照排序的顺序指定。例如，如果order1是C（1,3,2），并order2是C（1,2,3），则样本配对是A1-B1，B2，A3，A2-B3，A和B群1 2组群内。
The fold changes are difference between averaged subgroup1 expression vs averaged subgroup2. If paired t test is performed, the fold changes are calculated using each paired difference and take an average of paired difference.
褶皱的变化是平均subgroup1表达与之间的差异，平均subgroup2。如果进行配对t检验，倍数变化计算每个配对的差异，并采取平均配对差异。
值----------Value----------
None. But a number of plot and result files will be produced.
没有。但会产生一些图和结果文件。
作者（S）----------Author(s)----------
Y Andrew Sun
举例----------Examples----------
#- doPlotFCT(eset, "sampleGroup", c("liver", "muscle"))[ - doPlotFCT（ESET的“sampleGroup”，C（“肝”，“肌肉”））]
#- For a paired t test[ - 配对t检验]
#- doPlotFCT(eset, "sampleGroup", c("liver", "muscle"), order1 = c(1,2,3), order2 = c(1,3,2))[ - doPlotFCT（ESET的“sampleGroup”，C（“肝”，“肌肉”），order1 = C（1,2,3），order2 = C（1,3,2））]
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。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
|
发表于 2012-2-25 10:56:18
