Hey guys,
I am trying to use the normalize.loess() function as used in this article
My aim is to normalize ChIP-seq data using the affymetrix package. Unfortunately, I am facing some unexpected errors when executing this line :
res <- normalize.loess(mat=coverage_file$V4, subset=1:nrows(fly_coverage))
Error in matrix(0, II, J): non numeric matrix extent error
My coverage_file is a dataframe containing merged reads from fly and human ChIP-seq. The 4th column I'm trying to use contains the normalized values of the read counts. I want to apply local regression on these values.
Using the as.matrix() function does not help and gives me the following error :
Error in mat [,k] : out of bounds index
Have you had this issue and do you know how to solve it ?
Best wishes
