I extracted beta-scores from a MLE file generated by MAGeCK_VISPR and run it on ReadBeta with transforming gene symbol to Entrez gene id. However, When running NormalizeBeta on beta scores file, I got a error as follows:
command I used fmlebetaessential <- NormalizeBeta(fmlebeta, c(fmlebeta$Rwith, fmlebeta$Rwithout), "cellcycle")
2019-03-21 12:29:35 # Normalize beta scores ... Error in .subset(x, j) : only 0's may be mixed with negative subscripts
Could you please help me with a solution for this?