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)
csv文件截图-2
csv文件截图-1
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!
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