I have to perform quality control of methylation data from 96 samples on which we realized EPIC array (Illumina) technology. For doing it, there are two possibilities: using Genome Studio software (supplied by Illumina) or using R packages.
I am inclined to use R packages, since I am more confident with R software. So, I found RnBeads package, which is very useful for solving my task.
Some colleagues of mine have previously worked with Genome Studio, and they performed quality control by comparing the number of detected CpG islands satisfying detection p-value of 0.05 and 0.01 between all the samples.
To be clear, after preparing the project with Genome Studio software, they obtained a Sample Table (see p 71 of the manual at this link https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/genomestudio/genomestudio-2011-1/genomestudio-methylation-v1-8-user-guide-11319130-b.pdf), in which there were several columns. Among these column, there was one with detected CpG islands with p-value < 0.01 for each analysed sample, whilst another column reported the number of detected CpG islands with p-value < 0.05 for each sample, like the following example:
SAMPLE DETECTED CpG (0.01) DETECTED CpG (0.05) A1 866,789 867,789 A2 865,999 866,999 A3 850,001 851,001 A4 860,995 861,995 A5 858,098 859,098 A6 851,001 852,001 A7 855,987 854,987
The previous table is an example with 7 samples. This is the aspect of the Sample table reported in Genome Studio.
Now, my question is: is it possible to know the number of detected CpG islands satisfying detection p-value of 0.05 and 0.01 for each sample also with RnBeads? Or is it possible only with Genome Studio?