Hi!
I played around with the Illumina mouse demo data and ENmix. The following code worked for me and you should end up with normalized beta values for subsequent limma analysis (or DMR analysis folowing the ENmix vignette).
#setwd()
#download the Infinium_Mouse_Methylation_v1.0_A1_GS_Manifest_File.csv file from Illumina HP to working directory (= directory with idats and .csv)
library(ENmix)
library(geneplotter)
library(limma)
mf="Infinium_Mouse_Methylation_v1.0_A1_GS_Manifest_File.csv"
rgSet <- readidat(path = getwd(),manifestfile=mf,recursive = TRUE)
######Raw data QC and inspection
plotCtrl(rgSet)
mraw <- getmeth(rgSet)
multifreqpoly(assays(mraw)$Meth+assays(mraw)$Unmeth,xlab="Total intensity")
beta_raw<-getB(mraw)
anno=rowData(mraw)
beta1=beta_raw[anno$Infinium_Design_Type=="I",]
beta2=beta_raw[anno$Infinium_Design_Type=="II",]
multidensity(beta_raw,main="Multidensity")
multifreqpoly(beta_raw,main="Multifreqpoly",xlab="Beta value")
multidensity(beta1,main="Multidensity: Infinium I")
multifreqpoly(beta1,main="Multifreqpoly: Infinium I",xlab="Beta value")
multidensity(beta2,main="Multidensity: Infinium II")
multifreqpoly(beta2,main="Multifreqpoly: Infinium II",xlab="Beta value")
head(beta_raw,15)
######Process data
beta=mpreprocess(rgSet, nCores=6)
beta11=beta[anno$Infinium_Design_Type=="I",]
beta22=beta[anno$Infinium_Design_Type=="II",]
multidensity(beta,main="Multidensity")
multifreqpoly(beta,main="Multifreqpoly",xlab="Beta value")
multidensity(beta11,main="Multidensity: Infinium I")
multifreqpoly(beta11,main="Multifreqpoly: Infinium I",xlab="Beta value")
multidensity(beta22,main="Multidensity: Infinium II")
multifreqpoly(beta22,main="Multifreqpoly: Infinium II",xlab="Beta value")
head(beta,15)
######Continue with limma or DMR analysis
Hope that helps :)
Hi julia_geh. I am the maintainer for methylsuite. I'm happy to debug whatever might have been wrong 5 weeks ago with processing the mouse array IDATs. Please note that I just pushed an update that fixes some mouse bugs last week (v1.5.2) here: https://pypi.org/project/methylprep/
Hopefully that resolves your issue. But feel free to contact me (or post a github issue) if you find other errors.
Have you tried later versions of
methylsuite
/methylprep
(python) with the mouse arrays? Early versions of the software was based on earlier manifests from the manufacturer that contained errors, but methylprep versions > 1.5.x should run.Hi.
I am having problem in the following processing command...
beta=mpreprocess(rgSet, nCores=1)
"NA samples with percentage of low quality CpG value greater than 0.05 or bisulfite intensity less than NaN NA CpGs with percentage of low quality value greater than 0.05 Ploting qc_sample.jpg ...Error in plot.window(...) : need finite 'ylim' values In addition: Warning messages: 1: In min(x) : no non-missing arguments to min; returning Inf 2: In max(x) : no non-missing arguments to max; returning -Inf"
I'm working on the following demo datasheet.. https://webdata.illumina.com/downloads/productfiles/mouse-methylation/infinium-mouse-methylation-demo-dataset.zip
with the manifest... https://jp.support.illumina.com/downloads/infinium-mouse-methylation-gene-probe-annotation.html (Note: replaced all "2" by "II" and all "1" by "I" in the Infinium_Design_Type column)
Does anyone have any idea about the error occurred? Where I can make changes to the 'ylim'?
Did you get this figured out? I am having the same error in R.