Question: writing result from vsn package
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5.1 years ago by
A3.9k
A3.9k wrote:

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

R • 1.5k views
ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by A3.9k
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