Entering edit mode
10 months ago
mnx0723
•
0
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)
Hey, you should not perform DE analysis using DESeq2 for these data. They do not have raw count values.