如题所述
第1个回答 2022-06-30
GSEA支持的数据格式
官网给出的数据格式：
Data formats
1.1 GCT: Gene Cluster Text file format (*.gct)
tab键分割的文档
1.4 TXT: Text file format for expression dataset (*.txt)
tab键分割的文档
表型文档定义了表达文档中样品的表型标签，使用空格或tab隔开；表型文档分为类别型与连续性；
2.1 CLS: Categorical (e.g tumor vs normal) class file format ( .cls)
连续性表型文件包含一个或多个类别；
#numeric
#AFFX-BioB-5_st
206.0 31.0 252.0 -20.0 -169.0 -66.0 230.0 -23.0 67.0 173.0 -55.0 -20.0 469.0 -201.0 -117.0 -162.0 -5.0 -86.0 350.0 74.0 -215.0 193.0 506.0 183.0 350.0 113.0 -17.0 29.0 247.0 -131.0 358.0 561.0 24.0 524.0 167.0 -56.0 176.0 320.0
#AFFX-BioDn-5
75.0 142.0 32.0 109.0 -38.0 -80.0 62.0 39.0 196.0 -42.0 199.0 49.0 171.0 327.0 115.0 -71.0 85.0 80.0 270.0 182.0 208.0 -94.0 292.0 233.0 34.0 0.0 59.0 233.0 48.0 466.0 -7.0 -96.0 297.0 38.0 208.0 -15.0 30.0 357.0
第一行："#numeric"指明这是一个连续性标签
剩下的数据就是连续性标签表型：
每两行定义一个分类：
第一行：类别名，如 #AFFX-BIOB-5_st
第二行：一行对应表达数据中每个样品的值
For a continuous phenotype label, the values for the samples define the phenotype profile. The relative change in the values defines the relative distance between points in the phenotype profile. In the example shown above, the sample values for the two phenotype labels are gene expression values. The phenotype profile is the expression profile for a gene and is used to find gene sets correlated with that gene. For a time series experiment, you would choose sample values that define the desired expression profile. The example shown below assumes that you have five samples taken at 30 minute intervals. The first phenotype label defines a phenotype profile that shows steadily increasing gene expression; the second defines a profile that shows an initial peak and then gradual decrease:
#numeric
通常有两种格式：
GMX中每列是一个基因集，包含名字，描述，基因集中的基因；
GMT中每行是一个基因集，包含名字，描述，基因集中的基因；
3.1 GMX: Gene MatriX file format (*.gmx)
3.2 GMT: Gene Matrix Transposed file format (*.gmt)
4.1 CHIP: Chip file format (*.chip)
文件中包含了对芯片的注释；
第一行是每一列的列名：
文件中必须包含的三列：Probe Set ID Gene Symbol Gene Title
The GENE_SYMBOL.chip file contains one additional column, Aliases, which is not shown here. When a gene is identified by more than one HUGO gene symbol, the Gene Symbol column contains the gene symbol that appears in the GSEA reports and the Alias column identifies other gene symbols used to reference the same gene. If a gene set or chip annotation file contains a gene in the Alias column, GSEA automatically converts it to the gene in the Gene Symbol column.
The rest of the file contains data for each probe set ID used in the microarray.
Line format: (probe set id) (tab) (gene symbol) (tab) (gene title)
5.1 RNK: Ranked list file format (*.rnk)
RNK这种格式文件中存放的是可排序的基因列表。下图就是一个例子展示，第一列是基因名，第二列是用于基因列表排序统计学数值。
官网给出的数据格式：
Data formats
1.1 GCT: Gene Cluster Text file format (*.gct)
tab键分割的文档
1.4 TXT: Text file format for expression dataset (*.txt)
tab键分割的文档
表型文档定义了表达文档中样品的表型标签，使用空格或tab隔开；表型文档分为类别型与连续性；
2.1 CLS: Categorical (e.g tumor vs normal) class file format ( .cls)
连续性表型文件包含一个或多个类别；
#numeric
#AFFX-BioB-5_st
206.0 31.0 252.0 -20.0 -169.0 -66.0 230.0 -23.0 67.0 173.0 -55.0 -20.0 469.0 -201.0 -117.0 -162.0 -5.0 -86.0 350.0 74.0 -215.0 193.0 506.0 183.0 350.0 113.0 -17.0 29.0 247.0 -131.0 358.0 561.0 24.0 524.0 167.0 -56.0 176.0 320.0
#AFFX-BioDn-5
75.0 142.0 32.0 109.0 -38.0 -80.0 62.0 39.0 196.0 -42.0 199.0 49.0 171.0 327.0 115.0 -71.0 85.0 80.0 270.0 182.0 208.0 -94.0 292.0 233.0 34.0 0.0 59.0 233.0 48.0 466.0 -7.0 -96.0 297.0 38.0 208.0 -15.0 30.0 357.0
第一行："#numeric"指明这是一个连续性标签
剩下的数据就是连续性标签表型：
每两行定义一个分类：
第一行：类别名，如 #AFFX-BIOB-5_st
第二行：一行对应表达数据中每个样品的值
For a continuous phenotype label, the values for the samples define the phenotype profile. The relative change in the values defines the relative distance between points in the phenotype profile. In the example shown above, the sample values for the two phenotype labels are gene expression values. The phenotype profile is the expression profile for a gene and is used to find gene sets correlated with that gene. For a time series experiment, you would choose sample values that define the desired expression profile. The example shown below assumes that you have five samples taken at 30 minute intervals. The first phenotype label defines a phenotype profile that shows steadily increasing gene expression; the second defines a profile that shows an initial peak and then gradual decrease:
#numeric
通常有两种格式：
GMX中每列是一个基因集，包含名字，描述，基因集中的基因；
GMT中每行是一个基因集，包含名字，描述，基因集中的基因；
3.1 GMX: Gene MatriX file format (*.gmx)
3.2 GMT: Gene Matrix Transposed file format (*.gmt)
4.1 CHIP: Chip file format (*.chip)
文件中包含了对芯片的注释；
第一行是每一列的列名：
文件中必须包含的三列：Probe Set ID Gene Symbol Gene Title
The GENE_SYMBOL.chip file contains one additional column, Aliases, which is not shown here. When a gene is identified by more than one HUGO gene symbol, the Gene Symbol column contains the gene symbol that appears in the GSEA reports and the Alias column identifies other gene symbols used to reference the same gene. If a gene set or chip annotation file contains a gene in the Alias column, GSEA automatically converts it to the gene in the Gene Symbol column.
The rest of the file contains data for each probe set ID used in the microarray.
Line format: (probe set id) (tab) (gene symbol) (tab) (gene title)
5.1 RNK: Ranked list file format (*.rnk)
RNK这种格式文件中存放的是可排序的基因列表。下图就是一个例子展示，第一列是基因名，第二列是用于基因列表排序统计学数值。
