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 Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 13 specialties. Named to FORTUNE? Magazine's "100 Best Companies to Work For?" list eight years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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 Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 13 specialties. Named to FORTUNE? Magazine's "100 Best Companies to Work For?" list eight years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.