[BioC] Can't get ComBat in SVA running after SCAN.UPC

[Peterson, Leif]

SCAN.UPC was used to normalize Hu-133A arrays, and the run worked fine using the syntax:

normalized=SCAN(celFilePath, "output_file.txt")

Next, I would like to implement ComBat in SVA using the syntax:

library("sva")
exprdata<- as.matrix(read.table("output_file.txt", header=T))
batch<- as.matrix(read.table("batch.txt", header=T))
ComBat(exprdata,batch)

(FYI, "exprdata" exists in memory as a 22283x919 double matrix, and "batch" is  919 x 1 character matrix with the GEO dataset name, e.g., "GSE1456") 

However, an exception is being thrown in ComBat which reads as follows:

> ComBat(data,batch)
Reading Sample Information File
Error in file(file, "rt") : invalid 'description' argument

Any suggestions?  

LP

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