Question: (Closed) Error when running MEDIPS
1
gravatar for zengxi.hada
2.9 years ago by
zengxi.hada70
Hong Kong
zengxi.hada70 wrote:

Dear all,

I was running MEDIPS. I use the following command lines. But error occurs, which is showed below. I really appreciate it if someone can help me to solve it. Thanks.

library(MEDIPS)

bam.file.HIV.Rep1.MeDIP = "Jurkat_HIV.sort.rmdup.bam"

bam.file.HIV.Rep1.MeDIP = "Jurkat_HIV.sort.rmdup.bam"

library(BSgenome.Hsapiens.UCSC.hg38)

HIV_MeDIP = MEDIPS.createSet(file=bam.file.HIV.Rep1.MeDIP, BSgenome="BSgenome.Hsapiens.UCSC.hg38", uniq=1e-3, extend=300, shift=0, window_size=100)

HIV5aza_MeDIP = MEDIPS.createSet(file=bam.file.HIV5aza.Rep1.MeDIP, BSgenome="BSgenome.Hsapiens.UCSC.hg38", uniq=1e-3, extend=300, shift=0, window_size=100)

CS = MEDIPS.couplingVector(pattern="CG", refObj=HIV5aza_MeDIP)

mr.edgeR = MEDIPS.meth(MSet1=HIV_MeDIP, MSet2=HIV5aza_MeDIP, CSet=CS, p.adj="holm", diff.method="edgeR", MeDIP="F", CNV=F, minRowSum=10)

Calculating genomic coordinates... Creating Granges object for genome wide windows... Preprocessing MEDIPS SET 1 in MSet1... Preprocessing MEDIPS SET 1 in MSet2... Differential coverage analysis... Extracting count windows with at least 10 reads... Execute edgeR for count data of 0 windows... (Neglecting parameter 'type') Creating a DGEList object... Apply trimmed mean of M-values (TMM) for library sizes normalization... There is no replication, setting dispersion to bcv^2 where bcv=0.01. Please consider http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf section 2.9. Calculating differential coverage... *Error in rownames<-(*tmp*, value = c("tag.1", "tag.0")) : length of 'dimnames' [1] not equal to array extent

In addition: Warning message: In edgeR::DGEList(counts = values[filter, ], group = edRObj.group) : Zero library size detected.*


software error R medip seq • 1.1k views
ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by zengxi.hada70
1
gravatar for zengxi.hada
2.9 years ago by
zengxi.hada70
Hong Kong
zengxi.hada70 wrote:

I found the problem myself. The problem is that the Chromosomes list are not the same between input bam file and BSgenome.Hsapiens.UCSC.hg38.

ADD COMMENTlink modified 2.4 years ago by Istvan Albert ♦♦ 80k • written 2.9 years ago by zengxi.hada70
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