R

我有一个来自illumina beadchip平台的mircarray数据集，我一直在使用它来检查3个治疗组之间的差异表达。在背景减法和归一化之后，我有一个Elist类的文件-如下所示

$E
                     A         B         C         D        E        F         
ILMN_1        9.678162  9.635665  9.420577  9.778417  9.521473  9.820778  
ILMN_2       11.458221 11.152161 11.158666 11.410278 11.416522 11.377062 
ILMN_3        9.385075  9.087426  9.230654  9.704379  9.720282  9.482488  
ILMN_4        9.909423  9.115123  9.693177 10.348670  9.896625  9.729896  
ILMN_5       11.826927 12.067796 12.165630 12.256113 12.061949 12.213470 

$genes
             SYMBOL
ILMN_1       Gene 1
ILMN_2       Gene 2
ILMN_3       Gene 3
ILMN_4       Gene 4
ILMN_5       Gene 5

我现在想创建一个Elist类的对象，它只包含由其基因符号选择的基因子集，以便生成子集的热图。我应该可以从那里管理热图

乙二醇

我试过了

subset=Elist[Elist$genes==cgene2，gene4，]让我们调用这个对象expr，而不是Elist类本身的名称：

require(limma)
expr <- new("EList"
            , .Data = list(structure(list(A = c(9.678162, 11.458221, 9.385075, 9.909423, 11.826927), 
                                          B = c(9.635665, 11.152161, 9.087426, 9.115123, 12.067796), 
                                          C = c(9.420577, 11.158666, 9.230654, 9.693177, 12.16563), 
                                          D = c(9.778417, 11.410278, 9.704379, 10.34867, 12.256113), 
                                          E = c(9.521473, 11.416522, 9.720282, 9.896625, 12.061949), 
                                          F = c(9.820778, 11.377062, 9.482488, 9.729896, 12.21347)), 
                                     .Names = c("A", "B", "C", "D", "E", "F"), 
                                     class = "data.frame", 
                                     row.names = c("ILMN_1", "ILMN_2", "ILMN_3", "ILMN_4", "ILMN_5")), 
                           structure(list(SYMBOL = c("Gene1","Gene2", "Gene3", "Gene4", "Gene5")), 
                                     .Names = "SYMBOL", 
                                     row.names = c("ILMN_1","ILMN_2", "ILMN_3", "ILMN_4", "ILMN_5"), 
                                     class = "data.frame")))

---

我是否遗漏了一个关于热图的问题，我看不到任何？

%in%而不是==？问题的热图部分在哪里？非常感谢回答-上面编辑的问题。非常感谢。工作真的很好。我已经编辑了要添加到热图请求中的问题。

require(limma)
expr <- new("EList"
            , .Data = list(structure(list(A = c(9.678162, 11.458221, 9.385075, 9.909423, 11.826927), 
                                          B = c(9.635665, 11.152161, 9.087426, 9.115123, 12.067796), 
                                          C = c(9.420577, 11.158666, 9.230654, 9.693177, 12.16563), 
                                          D = c(9.778417, 11.410278, 9.704379, 10.34867, 12.256113), 
                                          E = c(9.521473, 11.416522, 9.720282, 9.896625, 12.061949), 
                                          F = c(9.820778, 11.377062, 9.482488, 9.729896, 12.21347)), 
                                     .Names = c("A", "B", "C", "D", "E", "F"), 
                                     class = "data.frame", 
                                     row.names = c("ILMN_1", "ILMN_2", "ILMN_3", "ILMN_4", "ILMN_5")), 
                           structure(list(SYMBOL = c("Gene1","Gene2", "Gene3", "Gene4", "Gene5")), 
                                     .Names = "SYMBOL", 
                                     row.names = c("ILMN_1","ILMN_2", "ILMN_3", "ILMN_4", "ILMN_5"), 
                                     class = "data.frame")))

expr[ expr$genes$SYMBOL %in% c("Gene2", "Gene4"), ]