TCGA数据提取后用DESeq2作分析，结果得到log2foldchange全是1

zhuangrui_tea

TCGA数据提取后用DESeq2作分析，结果得到log2foldchange全是1，原因可能是什么？
代码如下：

[Python] 纯文本查看 复制代码

# 用DESeq2进行差异表达分析 
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq")
biocLite("pasilla")
biocLite("BioParallel")
library(limma)
library(DESeq2)
library(pasilla)

foldChange = 1
padj = 0.05
setwd("/Users/tea/Bioinformation/TCGA/work_space/DataTransformation")
rt = read.table("geneName_Matrix_Processed.csv",sep=",",header=T,check.names=F)
rt = as.matrix(rt)
dimnames=list(rownames(exp),colnames(exp))
countData = matrix(as.numeric(as.matrix(exp)),nrow=nrow(exp),dimnames=dimnames)
condition = factor(c(rep("normal",44),rep("tumor",502)))
colData = data.frame(row.names=colnames(countData), condition)
dds = DESeqDataSetFromMatrix(countData, DataFrame(condition), design= ~ condition ) 
head(dds)  
dds = DESeq(dds, parallel = T)   

library("BiocParallel")
register(MulticoreParam(16)) 

res = results(dds, parallel = T) 
write.csv(res,file= "DESeq2_results_out.csv", row.names = T)

打开csv文件后，log2foldchange一列全是1...不知道问题可能出在哪里？谢谢大家！

海底钢琴

[Python] 纯文本查看 复制代码

rt = read.table("geneName_Matrix_Processed.csv",sep=",",header=T,check.names=F)
rt = as.matrix(rt)
dimnames=list(rownames(exp),colnames(exp))
countData = matrix(as.numeric(as.matrix(exp)),nrow=nrow(exp),dimnames=dimnames)

感觉这个程序跑不通，变量exp是哪里来的。