Epigenomics forum

Hi! Does anybody has encounter this problem?. I have updated my R and Rstudio version in windows,

Hi, Just wondering if anyone has encountered this issue whilst running Rnbeads before? 2022-02-18 14:

Dear Tian: I have tried to set.seed(somenumber) at the very beginning of my program, but still I get

Hi, Can any one please guide me on how to make a plot like that? Best, Ayesha

Hi, I am using Gviz package for plotting DMRs. So far I have successfully created attrack, itrack and

Hi all, I am working with Gviz R package and getting the following error > itrack <-

Dear Katie, I am happy to help. Yes, the number of CpGs per region also has an influence on the

Hi Michael, No worries. Datasets used in the analysis are below. Let me know if you'd like me to

I found a guy had the same issule, So can it be sure it's a bug? https://github.com/epigen/

Dear Tian: I want to extract an average beta value at the gene level for each sample. This could be

Hi all, Attached is my SVD plot, how to interpret it? Any suggestion would be appreciated. Best,

Hello everyone, I am using DMRcate to detect differentially methylated regions between two groups

Hi Nadezhda, GO is not really related to pathways, it is rather a collection of associated terms (ie

Dear Michael, I took the first two suggestions above and everything seems to be working so far! I

Hi Peter, I am happy that at least parts of the analysis are correctly configured. Indeed, the issue

Dear Nadezhda, From the output you provided, I cannot certainly judge what the issue is, and can only

Dear Pawan, The minimum requirement for RnBeads import are the columns Chromosome, Start, End, Total

This is much more of a conceptual question, but I'm currently trying to understand the state of

Hi Elaine, You should use the t-values (since they are additive, while the p-values are not). You can

Hi, 1) Currently, the GUI only permits to use the default region sets. For including the 200bp you

Hi Adrian, Are you using the BED files exported by RnBeads? If so, BED files have been standardized

Dear Fabian, Indeed, this is the solution to the issue. Thank You very much! Best, Adrian On Tuesday,

Hi, I would like to use the hyper and hypo methylated regions per sample and I am interested in

I am trying to run an analysis with ERRBS data with the 'bismarkCytosine' data format. First,

Apologies for the recent proliferation of spam on the Epigenomics Forum. I have now banned a number

Hi! I have done damage to my DNA using too much methylfolate. Some of my symptoms are already much

I used the following code to try and run an EWAS: ewas <- cpg.assoc (betas, phenotype_final$

I suppose the problem was that in previous analysis I set another differential.comparison.columns. I

Hi all, I am looking for differentially methylated positions and regions within a set of samples that

I am currently using the IlluminaHumanMethylationEPICanno to annotate my CpG sites with their nearest