全部代码如下：

exprSet=exprs(gset)

boxplot(exprSet)

boxplot(exprSet,outline=FALSE, notch=T,col=group_list, las=2)

library(limma) 

exprSet=normalizeBetweenArrays(exprSet)

boxplot(exprSet,outline=FALSE, notch=T,col=group_list, las=2)

exprSet=as.data.frame(exprSet)

ex <- exprSet

qx <- as.numeric(quantile(ex, c(0., 0.25, 0.5, 0.75, 0.99, 1.0), na.rm=T))

LogC <- (qx[5] > 100) ||

  (qx[6]-qx[1] > 50 && qx[2] > 0) ||

  (qx[2] > 0 && qx[2] < 1 && qx[4] > 1 && qx[4] < 2)

if (LogC) { ex[which(ex <= 0)] <- NaN

exprSet <- log2(ex)

print("log2 transform finished")}else{print("log2 transform not needed")}

GPL_anno <-data.table::fread("GSE68619_family.soft",skip ="ID",data.table = F)

library(dplyr)

library(tidyr)

probe2symbol_df <- GPL_anno %>% 

  dplyr::select(ID,gene_assignment) %>% # 选择GPL_anno的ID列和gene_assignment列

  filter(gene_assignment != "---") %>%  # 删掉gene_assignment列是"---"的，因为啥也没有

  separate(gene_assignment,c("drop","symbol"),sep="//") %>% # 根据"//"分割，分割得到的前两个命名为"drop"和"symbol"

  dplyr::select(-drop) # 把“drop”去掉

colnames(probe2symbol_df) <-c("probeset","symbol")

probe2symbol_df=as.character(probe2symbol_df)

##################以下代码运行后开始报错

library(dplyr)

library(tibble)

exprSet <- exprSet %>% 

  rownames_to_column(var="probeset") %>% 

  #合并探针的信息

  inner_join(probe2symbol_df,by="probeset") %>% 

  #去掉多余信息

  select(-probeset) %>% 

  #重新排列

  select(symbol,everything()) %>% 

  #求出平均数(这边的点号代表上一步产出的数据)

  mutate(rowMean =rowMeans(.[grep("GSM", names(.))])) %>% 

  #去除symbol中的NA

  filter(symbol != "NA") %>% 

  #把表达量的平均值按从大到小排序

  arrange(desc(rowMean)) %>% 

  # symbol留下第一个

  distinct(symbol,.keep_all = T) %>% 

  #反向选择去除rowMean这一列

  select(-rowMean) %>% 

  # 列名变成行名

  column_to_rownames(var = "symbol")

错误：‘x'和'y’must  share the same src ,set 'copy'=TRUE(may be slow)

Run `rlang::last_trace()` to see the full context.

> rlang::last_trace()

<error/rlang_error>

`x` and `y` must share the same src, set `copy` = TRUE (may be slow).

Backtrace:

     x

  1. \-`%>%`(...)

  2.   +-base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))

  3.   \-base::eval(quote(`_fseq`(`_lhs`)), env, env)

  4.     \-base::eval(quote(`_fseq`(`_lhs`)), env, env)

  5.       \-`_fseq`(`_lhs`)

  6.         \-magrittr::freduce(value, `_function_list`)

  7.           \-function_list[[i]](value)

  8.             +-dplyr::inner_join(., probe2symbol_df, by = "probeset")

  9.             \-dplyr:::inner_join.data.frame(., probe2symbol_df, by = "probeset")

 10.               \-dplyr::auto_copy(x, y, copy = copy)

 11.                 \-dplyr:::glubort(...)