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I have a data frame consisting of 1893 p-values that I convert to qvalues using the R package qvalue:

pvals <- read.table("p_values.csv",header=T,sep=",",dec=".")

The qvalue manual states you can directly plot (using the qplot function) the output of the qvalue function by:

qobj <- qvalue(pvals)
qplot(qobj)

However this results instead in an error:

Don't know how to automatically pick scale for object of type qvalue. Defaulting to continuous Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) : cannot coerce class ""qvalue"" to a data.frame

Anyone have an idea how to fix this and make qplot plot the output of the qvalue function?

sk1985
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  • You should check the class of `qobj`. If its class is not compatible with `qplot`, you need to modify `qobj` to fit `qplot` requirements. –  Nov 10 '15 at 10:43

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