i want to remove unwanted variation from mi RNA raw read count data set,i have two sample one is control and other is main data, i tried to run following example: x1<-RUVg(x = more100,cIdx = migenes,k = 1,drop = 0) x=migenes is main data which has 2234 obs and 90 sample along with gene id cidx = migenes is negative control sample which has 641 obs with 90 sample along with gene id

and got error ::Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘RUVg’ for signature ‘"data.frame", "data.frame", "numeric"’** am i running code in correct way?

By definition, no. If you only have two samples then there is no unwanted variation to remove! In other words, the unwanted variation that RUV is intended to remove is between-sample variation (where by between-sample we really mean 'between samples from the same group'). Since you only have one sample per group, there is no variation between samples from the same group, hence no variability to remove.