Hi everybody,

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?