Dear Jong hwan kim,

it appears that your hMeDIP data cannot be modeled with the CpG dependent
calibration curve and linear regression. Therefore, I recommend to set the
MeDIP parameter of the MEDIPS.meth  function to FALSE when you are
processing hMeDIP data. Please note, you will not receive CpG density
normalized rms data when MeDIP=FALSE, but you still get your genome wide
read coverage (counts, rpkm), and you will be able to calculate
differential coverage.

Lukas




On Mon, Jan 6, 2014 at 3:26 AM, 김종환 <kkjjhhk@naver.com> wrote:

> Dear Lukas and Bioconductors,
>
>
>
> I’m using MEDIPS version 1.12.0 and analyzing MBD seq data and hMeDIP data.
>
>
>
> Sample is a Mouse stem cell and have same Input data on MBD seq and hMeDIP
> seq.
>
>
>
> It was fastq file, paired - end and I’m mapping on mm10, using bwa.
>
>
>
> And I read about error on previous version, contain unmapped error on bam
> file,
>
>
>
> So I use -F 4 options and get removed unmapped read bam files.
>
>
>
> Same preprocessing on MBD seq and hMeDIP data.
>
> Using same script refer manuscript MEDIPS, and can get DMRs on MBD seq, but
> I cant get hMeDIP seq.
>
>
>
> I don’t know why these happening.
>
>
>
> It normally load data and also saturation, seqCoverage analysis doing well.
>
>
>
> But when I get a `mr.edgeR`, it show errors
>
>
>
> > mr.edgeR = MEDIPS.meth(MSet1 = CD4_MeDIP, MSet2 = CD8_MeDIP, CSet = CS,
> ISet1 = MBD_Input, ISet2 = MBD_Input, p.adj = "bonferroni", diff.method =
> "edgeR",  prob.method = "poisson", MeDIP = T, CNV = F, type = "rpkm",
> minRowSum = 1)
>
> Calculating genomic coordinates...
>
> Creating Granges object for genome wide windows...
>
> Preprocessing MEDIPS SET 1 in MSet1...
>
> Calculating calibration curve...
>
> Performing linear regression...
>
> Error in 1:max_signal_index : argument of length 0
>
>
>
>
>
> I’m trying to find errors, sort bam files, include bam index files or
> exclude index files, and mapping again using bwa.
>
>
>
> Why these happening?
>
>
>
> Thanks,
>
> Jong hwan kim.
>
>
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>
>
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