Dear All Biostars, I desperately need your help! I am really new in Methylation in rare diseases subject and have no idea how to start the analysis. I want to recreate results by working on the GEO89353 data. There are raw data available, and matrix. I want to avoid the normalization procedure and so on. I want to use R example by creating a plot with methylation fraction (Beta value) and genomic location. I even don't how to calculate the Beta value or where should I find it. I am very sorry for being so dumb but I am really new in this subject, before I was working with NGS. I want to recreate results like in the paper with GEO89353. They used lima and metyAnalysis packages. I see lima is more to normalized data and so on.
I would be very very glad if someone could guide me step by step what should I do and how to analyse :(
Thank you in advance. Dorota
You've asked too many questions, and the situation summarizes to "do my job for me". You need to figure out what you want to do, and it will become a series of small steps, some of which you can solve and others you can ask more pointed questions. How to make a picture, or how to perform a calculation, are two separate questions. "What are the steps involved here" is not the sort of question a web forum can handle. Find a textbook or read some journal articles very carefully, the supplemental methods section of a good paper will tell you the steps they performed in order.
Thank you, will return with more detailed questions.
I searched PLOS One (because their articles are freely downloadable) for 'methylation' and found this article associating methylation patterns to exon usage. Read the methods section carefully and it should help you get a grasp of what to do.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0185224#sec018
Their Figure S5 is a pipeline diagram for analysis of sequencing data.
Thank you Karl:) You are a good men:)
Dear Karl, I was reading carefully publication you proposed to read and also again, paper my Boss wants me to do the analysis. I have question. I want to plot the graph where y will be the Methylation beta value, x genomic locations. I have beta values for one porband, father and one more and of course the controls of MXQ gene. The paper of Barbosa et al, provided at GEO: matrix file, SOFT file and Raw files. What I understand I have to use the matrix? What I mean I have a problem with understanding the x on the plot (genomic location). I know on which location of the gene they used, and I have such information but have no idea where to find the exact location to create the plot like they did. I have only the range of the genomic location.
Here is the link to the publication :enter link description here I want to recreate the Figure 1A.
I am very sorry I am still asking but I really don't know where to find the answer. ps. If you can and would like to help me here is email dorotabuczek81@gmail.com