Error while running Case study n. 3: Integration of methylation and expression for ACC
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hlee • 0
@c7b7fb2d
Last seen 4 months ago
United States

Hello,

I'm very new to TCGAbiolinks and I'm running through their given case studies in this link. I'm running case study 3, which is "Case study n. 3: Integration of methylation and expression for ACC" and as I'm running through the given code blocks, it's giving me an error and will not produce a volcano plot.

The first error was that there was an extra parenthesis in the na.omit line. I figured that as it was able to produce a figure in the case study, it would work but it didn't so I tried to take it out and the line did work. However, after that, when I run the code under #Volcano plot, it tells me that there is no "subtype_MethyLevel" in my data. I looked at it myself and it seemed that the tsv data didn't have a column and maybe that was why? But I'm not really sure how to fix it so that the code will be able to produce a volcano plot as shown in the link. Does anyone have any solution for me? Thank you for your time!

# na.omit
acc.met <- acc.met[rowSums(is.na(assay(acc.met))) == 0),]

# Volcano plot
acc.met <- TCGAanalyze_DMC(
    data = acc.met, 
    groupCol = "subtype_MethyLevel",
    group1 = "CIMP-high",
    group2="CIMP-low",
    p.cut = 10^-5,
    diffmean.cut = 0.25,
    legend = "State",
    plot.filename = "CIMP-highvsCIMP-low_metvolcano.png"
)
geneexpression methylation • 123 views
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