EnhancedVolcanop plot using GSE data

Question

[mnx0723]

I am very lacking in skills. Please advise on the code. volcanoplot is not drawn properly.

test <- getGEO("GSE58144", GSEMatrix = TRUE)
test <- test[[1]]
exprs_data <- exprs(test)
exprs_data[exprs_data < 0] <- 0
exprs_data <- round(exprs_data)
sample_info <- pData(test)
sample_info <- dplyr::select(sample_info,source_name_ch1, characteristics_ch1)


colData <- data.frame(condition = test$`condition:ch1`,
stringsAsFactors = FALSE)


dds <- DESeqDataSetFromMatrix(countData = exprs_data, colData = colData, design = ~condition)
dds <-DESeq(dds)
res <- results(dds)

EnhancedVolcano(
 res,
 lab = rownames(res),
 x = 'log2FoldChange',
 y = 'padj',
 xlim = c(-2, 2),
 title = 'Volcano Plot',
 pCutoff = 0.05,
 FCcutoff = 0.5,
 pointSize = 2.5)

[bk11]

Hey, you should not perform DE analysis using DESeq2 for these data. They do not have raw count values.