I am trying to perform loess normalization on a collection of RNA-seq datasets. Loven et al (Cell. 2012 October 26; 151(3): 476–482) claims to have used the affy package in R. I have the affy package installed but can't figure out how to specify my data files for 'mat' or 'subset' and I have no experience working in R. The affy manual provides instructions on how to load CEL files from microarray data, but my RNA-seq data is in the form of a tab delimited file on gene names and RPKM values.
Running the software without specifying the files gives the following:
> normalize.loess(mat, subset = sample(1:(dim(mat)[1]), min(c(5000,
+ nrow(mat)))), epsilon = 10^-2, maxit = 1, log.it =
+ TRUE, verbose = TRUE, span = 2/3, family.loess =
+ "symmetric")
Error in normalize.loess(mat, subset = sample(1:(dim(mat)[1]), min(c(5000, :
object 'mat' not found
How do I input my data/specify my data files? Is there information on the format of these two files (mat and subset)? Is there a better software package for this?
Any help would be appreciated!
-J