hi,
i have 8 CEL files and i am going to perform variance stabilization on them. then i did like below
> setwd("E:/Affy data")
> library(affy)
> library(vsn)
> celFiles <- list.celfiles()
> affyraw=ReadAffy(filenames = celFiles)
> affyraw.vsn2=vsn2(affyraw)
vsn2: 506944 x 8 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit.
but hereafter i don't know how to save the normalized file in a txt file because when i wrote like below i got these errors
> write.table(affyraw.vsn2, file = "arrayvsn.txt", dec = ".", sep = "\t", quote = FALSE)
Error in as.data.frame.default(x[[i]], optional = TRUE) :
cannot coerce class "structure("vsn", package = "vsn")" to a data.frame
> write.table(affyraw, file = "arrayvsn.txt", dec = ".", sep = "\t", quote = FALSE)
Error in as.data.frame.default(x[[i]], optional = TRUE) :
cannot coerce class "structure("AffyBatch", package = "affy")" to a data.frame
>
may you help me?
thank you