thank you for your email and please apologise my delayed response.
Abt Q1: Following the example shown at ?MEDIPS.correlation, everything works as expected:
correlation = MEDIPS.correlation(MSets=c(hESCs_MeDIP[], DE_MeDIP[]), 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.
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")
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)
Abt Q2: Please see the R script in the Supplementary Data file of our MEDIPS Bioinformatics Application Note.
All the best,
On 24 Dec 2015, at 06:08, chengyuanzhi1986 [bioc] <email@example.com<mailto:firstname.lastname@example.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=""/>:
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!
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