使用R语言进行gsva分析是遇到报错,如何解决?
运行gsva代码后提示报错,如下:
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘gsva’ for signature ‘"data.frame", "list"’
说明输入的数据类型是“data.frame”和"list",而gsva函数要求输入的是"matrix array”和"list",数据格式不正确出现报错。
解决方法如下:
exp.anno.z3 <- as.matrix(exp.anno.z2)
kegg2 <- gsva(exp.anno.z3, h.kegg_list, kcdf="Gaussian",method = "gsva")
运行后显示
kegg2 <- gsva(exp.anno.z4, h.kegg_list, kcdf="Gaussian",method = "gsva")
Estimating GSVA scores for 186 gene sets.
Estimating ECDFs with Gaussian kernels
|======================================| 100%
100%进度条提示gsva分析完成。
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