Question: [MEDIPS] Error in 1:max_signal_index : argument of length 0 - what does mean?
5.4 years ago by
김종환 • 20
김종환 • 20 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. [[alternative HTML version deleted]]
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