Hi everyone,
I am new to methylation data analysis and was now asked to analyze data (IDAT files) that was generated with the Infinium Mouse Methylation BeadChip Array. Because this array is quite new I cannot find best practices and a lot of packages for methylation data do not support mouse data in their standard workflow yet. I already tried minfi (R) and ENmix (R) but had problems loading the mouse manifest file. I also tried methylsuite (python) where I can load the data and the manifest but I get an error in the methylprep preprocess step. So, I cannot perform background correction here.
Is there anyone who has experience in analyzing Infinium Mouse Methylation BeadChip Array and who could provide some advice? This would help a lot!
Thanks in advance!
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.