[BioC] ComBat

Kovyrshina, Tatiana tkovyrshina at houstonmethodist.org
Mon Oct 28 17:22:34 CET 2013

I am trying to run ComBat on 4 batches of colorectal cancer that I got from the GEO website. I had success before with ComBat with different files, but for these R keeps giving me an error message:

> ComBat("output_file.txt","Sample Information File.txt")
Reading Sample Information File
Reading Expression Data File
Found 5 batches
Found 1 covariate(s)
Found 337 Missing Data Values
Standardizing Data across genes
Error in solve.default(t(des) %*% des) : 
  Lapack routine dgesv: system is exactly singular: U[1,1] = 0

I tried running it only on the first 100 genes, same problem. I tried only the first 10 genes, same problem. I tried using only 2 batches and same problem. I ran SCAN, but I cannot attach the output file from that because it is too big. I did attach my sample information file. 

Do you have any suggestions for me about what could be wrong?

Thank You!
Tatiana Kovyrshina

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.

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