FPKM和TPM都可以
问题如上。这些转换工具都需要输入一个基因表达矩阵,工具自带一个特征矩阵,举例如下,这个矩阵是用芯片表达基因计算的。芯片的数据我是直接拿来做输入的,tcga mRNA数据我不知道应该输入counts,FPKM还是TPM?
GeneSymbolB_cellsT_CD4T_CD8T_gamma_deltaNKMoMaDCgranulocytes
MARCH1 172.250 7.960 9.070 8.330 8.260 345.170 61.730
A2M-AS113.090 29.750 270.020 147.540 167.200 24.920 28.710
ABCB1212.070 37.140 64.540 516.280 190.630 27.320 19.200
ABCB4212.150 37.150 64.560 516.820 190.700 27.320 19.210
ADCYAP1339.040 49.950 75.530 43.090 72.970 45.150 58.040
ADGRE210.500 11.730 13.220 11.280 15.590 285.800 1217.330
ADGRE325.990 18.310 18.520 16.870 16.950 47.530 604.450
ADGRG342.550 36.120 50.400 47.640 100.770 38.780 716.130
ADRB2107.310 26.830 129.070 614.810 975.450 73.890 75.590
ADTRP16.040 219.240 21.290 10.940 13.210 16.020 14.220
AIM2725.770 126.460 35.170 105.860 39.670 77.170 20.270