Dear chengyuanzhi1986, thank you for your email and please apologise my delayed response. Abt Q1: Following the example shown at ?MEDIPS.correlation, everything works as expected: library(MEDIPSData) data(hESCs_MeDIP) data(DE_MeDIP) correlation = MEDIPS.correlation(MSets=c(hESCs_MeDIP[[1]], DE_MeDIP[[1]]), plot = FALSE) In your example, you are also processing the input samples included in the MEDIPSData package. These data sets need to be pre-processed. If you follow the code below, you will receive the correct correlation matrix and correlation plots will be generated within your current working directory. library(MEDIPS) library(MEDIPSData) library("BSgenome.Hsapiens.UCSC.hg19") data(hESCs_MeDIP) data(DE_MeDIP) bam.file.hESCs.Input = system.file("extdata", "hESCs.Input.chr22.bam", package = "MEDIPSData") bam.file.DE.Input = system.file("extdata", "DE.Input.chr22.bam", package = "MEDIPSData") BSgenome="BSgenome.Hsapiens.UCSC.hg19" uniq=1e-3 extend=300 shift=0 ws=100 chr.select="chr22" hESCs_Input = MEDIPS.createSet(file = bam.file.hESCs.Input, BSgenome = BSgenome,extend = extend, shift = shift, uniq = uniq, window_size = ws, chr.select = chr.select) DE_Input = MEDIPS.createSet(file = bam.file.DE.Input, BSgenome = BSgenome,extend = extend, shift = shift, uniq = uniq, window_size = ws, chr.select = chr.select) cor.matrix=MEDIPS.correlation(MSets=c(hESCs_MeDIP,DE_MeDIP,hESCs_Input,DE_Input),plot=T,method="pearson") Abt Q2: Please see the R script in the Supplementary Data file of our MEDIPS Bioinformatics Application Note. All the best, Lukas On 24 Dec 2015, at 06:08, chengyuanzhi1986 [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""/> User chengyuanzhi1986<https: support.bioconductor.org="" u="" 9421=""/> wrote Question: MEDIPS stable version problem<https: support.bioconductor.org="" p="" 76334=""/>: Dear Author, I found a something strange to me while using your MEDIPS stable packages with MEDIPSdata, here it is: Q1: run command "cor.matrix=MEDIPS.correlation(MSets=c(hESCs_MeDIP,DE_MeDIP,hESCs_Input,DE_Input),plot=T,method="pearson")", no plot is generated (BTW, Rstudio is used),and the cor.martix with NAs. Q2: which function can make the MA plot for the results of MEDIP.meth, the MA plot in your Bioinformatics article is pretty good? Thanks a lot! ________________________________ Post tags: MEDIPS You may reply via email or visit MEDIPS stable version problem