Hi all, I am working on ATAC seq data set, two cell types and two conditions, replicates >= 3 . read.csv2("SampleSheet041217.csv") diff <- dba(sampleSheet="SampleSheet041217.csv") diff_count <- dba.count(diff, minOverlap=2) 20 Samples, 649843 sites in matrix: ID Tissue Condition Treatment Replicate Caller Intervals FRiP 1 4471_64502 CD4p CLAp 0h 1 counts 649843 0.13 2 4471_64506 CD4p CLAp 0h 2 counts 649843 0.16 .. 20 99011_70076 CD8p CLAp 0h 6 counts 649843 0.18 diff_contrast_CD4 <- dba.contrast(diff_count,categories=DBA_CONDITION,block=diff$masks$CD4p) diff_analysis_CD4 <- dba.analyze(diff_contrast_CD4, method=DBA_DESEQ2) converting counts to integer mode gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates converting counts to integer mode DESeq2 multi-factor analysis gene-wise dispersion estimates mean-dispersion relationship Error in lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, : newsplit: out of vertex space In addition: There were 18 warnings (use warnings() to see them) I have read the error is something to do with maxk in locfit,default =100. It suggests to give a big value (> 500) to the parameter maxk when calling the function locfit. But I'm not sure how to edit this number in DiffBind. Could you help me solve the problem? Thanks a lot.
P.S. I also tried method=DBA_ALL_METHODS and got the same problem.