bioconductor上pvca的说明书是用golubEsets为例子,但是如果使用geo上下载的数据集的话,应该如何改写代码?
### code chunk number 2: example ################################################### library(golubEsets) library(pvca) data(Golub_Merge) pct_threshold <- 0.6 batch.factors <- c("ALL.AML", "BM.PB", "Source") pvcaObj <- pvcaBatchAssess (Golub_Merge, batch.factors, pct_threshold) ################################################### ### code chunk number 3: plot (eval = FALSE) ################################################### ## bp <- barplot(pvcaObj$dat, xlab = "Effects", ## ylab = "Weighted average proportion variance", ## ylim= c(0,1.1),col = c("blue"), las=2, ## main="PVCA estimation bar chart") ## axis(1, at = bp, labels = pvcaObj$label, xlab = "Effects", cex.axis = 0.5, las=2) ## values = pvcaObj$dat ## new_values = round(values , 3) ## text(bp,pvcaObj$dat,labels = new_values, pos=3, cex = 0.8)