I merged three datasets, two from same platform and one from a different platform, after merging I performed normalization and try to visualize using boxplot. But I am not getting a proper boxplot. I used the following codes:
# normalization of merged file #change to summarize experiment file mergenorm<- normalize(sum, norm.method = "quantile", data.type = "ma") #converted to matrix file for boxplot JM3<- assay(mergenorm) #boxplot for normalized data boxplot(exprs(JM3))
can anyone suggest what went wrong? or I can use any other plot?