在R中正确读取一个系列矩阵

Question

我在这里找到了 GSE60341_series_matrix.txt.gz ,当我把它读到R表中时,

x <-read.table("GSE60341_series_matrix.txt", fill = TRUE)

我得到了行中的所有信息.换句话说,我得到一个大小的矩阵(42977行和3列),而样本的数量应该是1951.所以理想情况下,我应该得到一个1951行的表和(一些k列代表每个样本).

打开文本文件让我,

    sapiens"    "Homo sapiens"  "Homo sapiens"  "Homo sapiens"  "Homo sapiens"  "Homo sapiens"  "Homo sapiens"  "Homo sapiens"  "Homo sapiens"  "Homo sapiens"  "Homo sapiens"  "Homo sapiens"  "Homo sapiens"  "Homo sapiens"  "Homo sapiens"  "Homo sapiens"  "Homo sapiens"  "Homo sapiens"  "Homo sapiens"  "Homo sapiens"
!Sample_title   "20120811_NC18_NC18_01" "20120811_NC18_NC18_02" "20120811_NC18_NC18_03" "20120811_NC18_NC18_04" "20120811_NC18_NC18_05"
    !Sample_characteristics_ch1 "stimulation: Unstim"   "stimulation: Activated"    "stimulation: IFNb" "stimulation: Unstim"   "stimulation: Activated"    "stimulation: IFNb" "stimulation: Unstim"   "stimulation: Activated"    "stimulation: IFNb" "stimulation: Unstim"   "stimulation: Activated"    "stimulation: IFNb" "stimulation: Unstim"   "stimulation: Activated"    "stimulation: IFNb" "stimulation: Unstim"   "stimulation: Activated"    "stimulation: IFNb" "stimulation: Unstim"   "stimulation: Activated"

"lane: 9"   "lane: 11"  "lane: 12"  "lane: 1"   "lane: 2"   "lane: 3"   "lane: 4"   "lane: 5"   "lane: 6"   "lane: 7"   "lane: 8"   "lane: 9"   "lane: 10"  "lane: 11"  "lane: 12"  "lane: 1"   "lane: 2"   "lane: 3"

在类别中的信息(lane,stimulation,Sample_title)串接为行,但我希望他们能在列.我可以有一个表格,其中行代表样本,列代表[Sample_title, stimulation]吗？

Answer 1

read.table 用于读取通用ASCII表格式,该文件采用NCBI Gene Expression Omnibus(GEO)使用的特殊格式.

这是你需要做的:

1. 通过将此代码粘贴到R中来安装GEOQuery包以读取GEO文件:

   source("http://bioconductor.org/biocLite.R")
   biocLite("GEOquery")
   

2. 使用以下行将包加载到内存中:

   library("GEOquery")
   

3. 编辑以下行,将工作目录中的完整路径放到引号内的文件中,以将数据作为对象读入内存gse:

   gse=getGEO(filename="~/Downloads/GSE60341_series_matrix.txt.gz")
   

4. 现在,如果你运行,View(gse)你会看到一个格式很好的表,在gse中有1950行.

   查看GEOquery文档以获取更多信息.