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

[Peterson, Leif]

Was able to get ComBat running, but it is attempting to write to an .xls file when done, which is throwing an exception.  How can I turn off the switch to write to an Excel file (.xls)?

Below is the output script and error message:

Reading Sample Information File
Reading Expression Data File
Found 5 batches
Found 0 covariate(s)
Standardizing Data across genes
Fitting L/S model and finding priors
Finding parametric adjustments
Adjusting the Data
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file 'Adjusted_output_file.txt_.xls': Permission denied


LP



________________________________________
From: Peterson, Leif
Sent: Monday, September 16, 2013 1:57 PM
To: bioconductor at r-project.org
Subject: Can't get ComBat in SVA running after SCAN.UPC

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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