TIDE数据标准化：R语言每行减去平均值—科研工具箱

最近很多人借TIDE账号，也有人问我如何进行数据标准化，按照网站说明，对于没有Control样本的测序数据，把表达量减去每个基因在所有样本中的平均值即可，即按照行计算平均值，再拿这一行所有表达量-该平均值。

#读取数据
Expr <- read.delim(\"TIDE_COAD.txt\",sep = \"\\t\",row.names = 1)

#使用apply函数
Expr <- t(apply(Expr, 1, function(x)x-(mean(x)))) 

一句代码就得到标准化矩阵

测试代码：

ma <- matrix(c(1:4, 1, 6:8), nrow = 2)
ma
#     [,1] [,2] [,3] [,4]
#[1,]    1    3    1    7
#[2,]    2    4    6    8
apply(ma, 2, function(x)x-(mean(x)))  ##按列计算
#     [,1] [,2] [,3] [,4]
#[1,] -0.5 -0.5 -2.5 -0.5
#[2,]  0.5  0.5  2.5  0.5
apply(ma, 1, function(x)x-(mean(x)))  ##按行计算
#     [,1] [,2]
#[1,]   -2   -3
#[2,]    0   -1
#[3,]   -2    1
#[4,]    4    3

转置一下即可：

t(apply(ma, 1, function(x)x-(mean(x))))
#     [,1] [,2] [,3] [,4]
#[1,]   -2    0   -2    4
#[2,]   -3   -1    1    3

apply函数参数帮助。

apply(X, MARGIN, FUN, …)

Arguments

X

an array, including a matrix.

MARGIN

a vector giving the subscripts which the function will be applied over. E.g., for a matrix 1 indicates rows, 2 indicates columns, c(1, 2) indicates rows and columns. Where X has named dimnames, it can be a character vector selecting dimension names.

FUN

the function to be applied: see ‘Details’. In the case of functions like +, %*%, etc., the function name must be backquoted or quoted.

…

optional arguments to FUN.