[BioC] error on microarray expression data

[Guest [guest]]

Dear users,

I met an error when I tried to run expression data after normalization. The first two columns are probe_id and gene symbol, the rest 12 columns are sample expression values. The file was saved in .csv format and read with function as:
datE=read.csv("expression.csv")

When I tried to use sampleNetwork() function to load the data, it generate an error:

Error in SampleNetwork(datExprT = datE, method1 = "correlation", impute1 =FALSE,  :
  expression matrix contains non-numeric data

I changed all expression dataset to numeric, using
datE.2=apply(datE[,3:14],2,as.numeric)

while running the function, it has the same error.

Could someone help to fix it? I do appreciate it.

Thanks a lot




 -- output of sessionInfo(): 

R version 3.0.0 (2013-04-03)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

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