In minfi quality control plots , density plot contains two parameters, one is beta value and another one is density. Are density parameter and CpG loci numbers the same?
I think it's the M value. The CN matrix is optional.
Do you mean that Y axis shows the M value's density?
I read the publication on the package this time instead of the user manual. The M value is the logit transformation of the Beta values.
Not sure which density plot function you are using. In the reference manual the input to the plotDensity function is the data object. It says the data object 'dat' is an RGChannelSet, a MethylSet or a matrix. We either use the getBeta function to get Beta values (for the first two) or we assume the matrix contains Beta values. So, not sure which two parameters you are referring to for the function.
Can you please provide some more information so I can help you?
in minfi user's guide in quality control part, below command is for QC plot. I have used it . Beta density plot is one of these plots, my question is about the Y axis in this plot. Y axis shows what?
qcReport(RGset, sampNames = pd$Sample_Name, sampGroups = pd$Sample_Group, pdf = "qcReport.pdf")
The manual says that it represents the raw, or unprocessed, Red and Green channel intensity values of the RGset. This is helpful to detect samples that may have issues or have failed.
Is this not what you see / get?
I only want to know the Y axis.
On page 7 of the user manual it says that it's the read and green channel measurements of the samples. So, it must be light intensity.
You could also say the Y-axis is the methylation and unmethylation values. I recommend you to read this paper: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btu049
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